Southern Italy 14 day Itinerary
 

We are planning to fly into Rome, in late Sept. and depart from either Naples, Bari or Palermo.
Please share your suggestions for an Itinerary for 14 days. This is our 1st trip to southern Italy.
What towns should be our home bases and for how many nights in each location?
Your advice on transportation from one location to another is appreciated (train or drive?)

Rome is not in southern Italy. Regions and cities here:

http://wikitravel.org/en/Southern_Italy

Also

http://wikitravel.org/en/Sicily

Well your first decision should be whether or not to include the island of Sicily - "southern Italy" is ambiguous and can include Sicily or not.

Do the 14 days you have include Rome, or is this all after Rome?

Lots and lots to see and do all ovr Sicily, less so in southern Italy, although obvious places like Naples/Pompeii, the Amalfi coast, etc. come to mind. Do not miss Naples.

Puglia is supposed to be beautiful and is getting hotter with tourism but still not trendy. Some beautiful towns and beautiful beaches to explore in that region. Check it out.

Or you could go straight from Rome to Sicily, skipping the in between. You could definitely fill up a week and a half to two weeks on the Mediterranean's largest island.

Been to Rome and would like to explore south. Just got good airfare into Rome.

As this is your first time in Italy I would suggest using the trains. We have done it often and they are great. Trenitalia is the main carrier in Italy and they have an English website which is quite easy to navigate.

The Puglia region is superb and there is lots to see on the
Gargano Peninsula. We spent a full week there and only scratched the surface. It is also cheaper than the well known regions like Amalfi coast.

However, this said, we were on the Amalfi coast in October last year and based ourselves in Maiori a non touristy town with lots of amenities, great hiking and superb restaurants.
It all depends what you want, crowds or a quieter travel experience. There are lots of Sita buses going along the coast every day and you can get very easily from one small town to another.

To really appreciate the area try and spend at least 4 nights in each of you home bases. That way to can unpack and relax instead of rushing from one place to another.

Italy is an amazing country - you will enjoy whatever you do.