I am not sure you even need a car unless you hope to day trip into CH. Given 6 days in the lakes, I would spend 4 on Lago Como and then consider a bus to the Swiss city of Lugano for 2 nites. You can get decent connections from there to MXP.

Have a look at the site http://www.vrbo.com/414960ha we are going to stay here ... The price is very reasonable and you can still get to the other parts of the lakes good luck and enjoy the luxury ps I love Milan and you will fill 2days there easily

This is personal preference, I think, but my preference would be to cut back your lake time and go to Switzerland or elsewhere for a few of your days. I spent 2.5 days on Lake Como (staying in Bellagio) in 2011, and that was about right for me. My international trips are few and far between, and if I want to just relax by the water, I can do that much more cheaply at home! Some people would stay for weeks, though, so it's a matter of what your group would like.

We found a couple of hikes, but it was harder to find information on those than I thought it would be. It just doesn't seem to be as emphasized as you might think in that area (perhaps it's different at the other lakes). The friend I was with said "I think people come here to drink wine and look at the lake." We ended up hiking up a cobblestone path to the castle above Varenna, then back down via Fiumelatte. On our second full day, we went to Villa Carlotta. It was great for a couple of days of relaxation.

if you want to stay in Milan so as to see the Last supper, can i suggest putting 2 nights in Milan at the end of the trip; this will give you a day to see the Last Supper and anything else you want to see, and put you in the right place for flying home.

use your first day when you may be suffering from jetlag to travel to your first destination.

Consider Lake Maggiore in addition to Lake Como. It's closer to Malpensa(MXP) for your departure. Two nights in Milan gives you one day so I would do the two nights...Duomo, La Scala, Galleria Victor Emmanuelle, The Last Supper..just a few things to see in your one day there.

Thank you, everyone! Based on the feedback, we revised the itinerary to the following (still work in progress):
Thursday, 05/23, am - arrive to Milan, get to Bellagio
Friday, Saturday, Sunday, Monday (1/2 d) - Bellagio and surroundings + day trip to Lugano + Bernina Express (?)
Monday (1/2), Tuesday, Wednesday (am) - Move to lake Maggiore, rent a car(?),
Wednesday - arrive to Milan in the eve
Thursday - Milan
Friday am - leave Milan

Now, questions:
1. My husband is concerned that by not getting a care for the entire duration of the trip, we might be limiting ourselves in being flexible, go to places on a whim, visiting places not on ferry routes, etc... So, how big of a problem is parking in/around Bellagio/Como and Maggiore
2. Is Lugano better explored from lake Como or lake Maggiore? Is Bernina Express doable in one day trip from either location?
3. Where to stay on lake Maggiore?
Thank you!

Forget the Bernina Express from those venues.
Lugano is better from Lago Como---actually from Menaggio on the west shore of Como---with a car I would stay there.

On Maggiore stay in Stresa www.stresa.net

If the weather is nice, Lake Como will be more crowded on the weekend than during the week. Perhaps someone can comment on Maggiore in comparison.

I agree with bobthenavigator that the western shore of Como is good when you have a car. (I would stay near Menaggio or Cadenabbia for easy access to the mid-lake ferries.) If you stay in Bellagio or Varenna, your exploring drives to the west and southwest are limited by the hours of the car ferry. However, there are some beautiful mountain drives from the eastern shore, and Bergamo is an easy day trip by train. (I would stay in or very near Varenna, again to be close to the mid-lake ferries and the train station.)

There are hikes in several areas all around the lake, but some are difficult and long-ish and more like trekking. If you want a trek, you can hike from Bellagio south to Rifugio Anna Maria or Rifugio Marina, both about 3 hours one way. The walk up to Castello Vezio above Varenna mentioned by jent103 is one of the better-known short walks. There is a falconry housed in the castle, so you should time you arrival to when the birds are released. If you don't want to walk back down the hill, there is a city bus stop.

http://www.castellodivezio.it/inglese/index.php

I had my heart set on staying in Bellagio but I suppose we could stay in Menaggio instead... would we miss out on anything by not staying in Bellagio? Any recommendations on the hotels there and in Stress?
Thank you!

The car is the problem---Bellagio is hard to access and a car is a liability---and an expense. It is a :15 ferry ride from Menaggio. You can stay in Bellagio if you want,but day trips by car would be difficult.

www.stresa.net Look at Luna del Porto

We liked staying in Bellagio. While it is the base of many "tourists" it is beautiful and there is a lot more going on at night than some of the other towns. Besides, there are tons of tourists everywhere. We stayed at the Hotel Metropole, which we loved because of the wonderful deck on the lake. We spent our afternoons cocktailing and watching the ferries coming and going.

The ferries were very easy and fast. You can get to all the other towns on the lake with no trouble. If you like house/garden tours there are several good ones that can eat up your time there. We especially enjoyed the speedboat tour around the lake, with a stop at Villa Barbianello.

We spent 3 nights in Bellagio and felt it was a good amount of time.
You can see the trip report here if youre interested.
http://www.fodors.com/community/europe/venice-bellagio-trip-report.cfm

Many people stay in Bellagio with a car. Some people are nervous drivers, but others are not. If you have your heart set on staying in Bellagio, stay there.

I don't think you need a car for either of your lake stays, but if for some reason you want to rent one, that's up to you.

I don't have any opinion about the Bernina Express because I've not taken it or perhaps you were thinking of the Palm Express, which makes a circuit that includes Lugano.

But I suggest that you visit Milan ahead of Lago Maggiore, and make Lago Maggiore your last stop before flying home because it is extremely easy to get to Malpensa airport from the lake. It is the same distance from the lake to the airport as it is from Milan to the airport. You can get a bus from the lake to the airport, or you can drive a car to the airport.

So maybe this would work for you:

Arrive Milan airport, go directly to Bellagio
Enjoy Bellagio and its surroundings, including possibly Lugano excursion
Take one-hour train ride from Varenna to Milan -- see sights in Milan (2 nights)
Take one hour train ride from Milan to Stresa on Lago Maggiore
Spend remaining time on lake until going to Malpensa airport (one hour away) to fly home

I don't think you need a car for any of the trip I just described.

I should have added that the town of Varenna on Lago di Como is a five-minute ferry ride from Bellagio, and a taxi will take you from the dock to the train station in Varenna if you don't want to walk uphill with your luggage.

You can also take a longer ferry ride from Bellagio down the lake to the town of Como, where you will easily find several trains going to Milan. Depends on how fast you want to get to Milan that day.

I think the car question all depends on what you end up doing. Three nights staying in Bellagio with no car was absolutely great for us - we took the ferry to Varenna one day and then over to Menaggio and Tremezzo the next. We had no need at all for a car. But if you want to do more exploring away from those towns, or are staying longer, a car would be good (and in that case you might not stay in Bellagio, as others have noted).

We have been in Bellagio with and without a car for several weeks. The ferry system takes you everywhere. If you want to have a car, Hotel Belvedere has parking which is scare in this town.

We have stayed on both Lake Como (Varenna and Bellagio and Lake Maggiore (Stresa and Connobio) on various trips. I do favor that over Milan just for the tranquillity of the lake versus the bustle of the city. What you like should determine where you stay (also have stayed in Milan.) I have liked all as I like Italy very much. I have also had the use of a car and found it to not be a problem. However, driving around the lakes can be tedious and slow due to curvy roads, fast Italian drivers and large quantities of vehicles including farm equipment.

You mentioned the Bernina Express. It is not very close to where you are in northern Italy. To me it is worth the journey as I have traveled twice. However, that can take up to 2 days of travel time. As an alternative, the Centovalli Railway is about a 2 hour, one way journey from Locarno on Lake Maggiore to Domodossola, Italy. Take a mid morning train from Locarno, have lunch in Italy and return in the afternoon. Not as spectacular as the Bernina but still very enjoyable.

Thiis will be our 5th visit to Italy so italian drivers/roads dont scare us really. Hubby drove in Amalfi, Sicily and Tuscany... this cannot be worse than Amalfi... or is it? My concern about having a car is mostly because of lack of parking, and it's coming up to be a bit pricey, at over 500 Euro for a week. Add parking fee and gas and we are looking at a significant expense which might be unnesesary. My concern about not having a car is about limiting ourselves to only places reachable by ferry/ public transportation... We like good food and dont mind to go out of the way for it so a car definitely comes handy for that... Decisions, decisions...
I have been looking more into Menaggio though and it seems to be more centrally located than Bellagio, for trips to Lugano and perhaps, even lake Maggiore... Is there a good selection of restaurants in/around Menaggio? And has anyone stayed in Hotel Royal there or can recommend any other hotel?
Thanks so much!

The roads around Lago di Como are definitely not as difficult as the Amalfi Drive. On weekends, they get plenty of traffic, however, and I think you are right to be concerned about parking. A day trip to Lugano, especially if you are just going there to visit the city, would be the kind of day trip where, even if I had a car, I would probably leave it parked at the hotel and take the bus, just to avoid parking costs and hassles in Lugano.

Like all popular tourist places, there are loads of restaurants all around the lake are they are very much a mixed bag, both when it comes to quality and when it comes to price. You need to do some research using guides that recommend the kind of food you like. But certainly when it comes to finding good restaurants, your chances are just as good in Menaggio as they are in Bellagio or anywhere around the lake. Menaggio is a very popular destination for weekend jaunts for people driving up from Milan, so you remember to make reservations if you track down restaurants you want to try (anywhere in the lakes, really, on a weekend).

If you decide to have a car, you might do better visiting Milan right at the top of the trip, and then leaving by train to rent your car in the town of Como and driving to your Lago di Como hotel. After that, drive to Lago Maggiore and take the car ferry from Laveno to Verbania, and then drive down the western shore of the lake to stay in Baveno or Stresa. From there, you would have an easy drive to Malpensa airport for your departure.

Figure out where you want to explore that can only be done by car and then decide if the expense (and the decision to stay somewhere other than Bellagio) is worth it to you. FWIW, we've stayed on Lake Como both with and without a car. You will not run out of things to see without a car. Besides the ferries, there are easy day trips by train from Varenna. Just be sure to know the Varenna-Bellagio ferry schedule if you're sleeping in Bellagio.

In Bellagio, look at the Residence Lalimonera apartments which have their own parking lot. If you decide to drive up the 'peninsula' to Bellagio (as opposed to either coastal road), make sure you have a good road map.

http://www.residencelalimonera.com/

I'm a fan of Milan, so I think 2 nights there would be great.

It depends on your budget for hotels.
The Grand Hotel Menaggio is a 4 star at the ferry dock that has seen better days but has the perfect location--and parking. The Hotel Du Lac[ there are 3 of them on Lago Como] is more reasonable and is right in the town square. The Hotel Bellavista has great views toward Bellagio and decent food. The Albergo Lenno is further south in Lenno but still on the west side. Good luck !

This may help---click on an image and select slide show.

http://www.slowphotos.com/photo/showgallery.php?cat=4442