Do you have guidebooks yet? For this trip, I'd recommend Lonely Planet guides. You need to look at maps and at transport options. Right now you have yourselves going from VN to Laos, back to VN then to Cambodia. This takes a lot of time and means you'll need a multi-entry visa for VN.

No doubt, you'll need to edit your itinerary some. So think about what is most important for you to do/see/experience on this trip.

You don't need a tour. Yes, private tours can be expensive because they have a guide with you all of the time - something you don't need. If you want a guide somewhere you can hire one on the spot.

Read some fo the trip reports here - there are many. You'll need to devore some time to information gathering. Once you have laid out an itinerary (come back and post it and we'll be glad to offer feedback), you might want to use an agent to price part of it. There are a couple of agencies in VN that peopole ahve had good experinces with that can often get good hotel prices (vietnamstay and tonkin come to mind) and there are internet booking sites for hotels that can save you a lot of money.

As you look for info on this site, you can go to the top of the page and sort by country. So if you choose Cambodia from the drop-down menu, you'll see all recent posts about Cambodia (and you'll se that the boat to Siem Reap is not recommended).

Also think about your route and flight possibilities, i.e can you go from say VN to Luang Prabang direct (to save time) Or do you do Cambodia before then as there is a direct flight from SR to LP (i also look at the places i want to go then check out flight routes).
Sounds like a great trip and once honed the itinerary will be very exciting i am sure.
Good luck (and enjoy the planning) you are going to some AMAZING places - Luang Prabang/Hanoi are 2 of my favourites.

I booked everything myself, some at last minute with my laptop. It's natural to feel overwhelmed in the beginning but slowly things fall into place. I also bought LP S.E Asia. You can ask questions on http://www.travelfish.org, I think you can find more info there than here. I use tripadvisor for hotel reco, some are obvious bias and faked but for the most part you can trust the comments there. Hope this helps.

It costs about US$55 to hire a car with driver for the two of us to go from Hoi An to Hue and a stop on the China beach was included.
Kayaking is included in all Ha Long cruise. i like less cabins and less people. You can book that cruise with the front desk if you are not choosy when you arrive Hanoi. if you want the most popular, book in advance. You can book just about anything like restaurants and small tours with the front desk.

In terms of general planning, as mohan has said travelfish is your best bet. Also, you could use one of the pre-prepared itineraries from one of the big tour agencies such as http://www.intrepidtravel.com/trips/LRP by playing around with the various trips you can design your own and they will have done a lot of the hard work for you.

IMO Ba Be is one of the most beautiful places in North Vietnam. It would I suppose be possible to get there by public transport, it is time consuming (the best part of from Hanoi in a private car). If you are short on time it is probably easier to book a tour from one of the agencies in the Old Quarter - 3 days /2nts is about right. I think we paid around $250 for two of us all inc. http://www.travelpod.com/travel-blog-entries/candcthai/1/1202972280/tpod.html

it is possible to get there from Sapa/lao Cai but expect very rough dirt roads and it may prove difficult to get back to Hanoi if not pre arranged.

As an alternative to Sapa you may want to consider the Mai Chau valley as a side trip from Hanoi. Arguably more beautiful than Sapa but much closer.

http://www.travelpod.com/travel-blog-entries/candcthai/3/1250748042/tpod.html