My Mom and I are planning on traveling to Italy at the beginning of October. We want to fly into Rome then visit Bari (where her mother is from). We are thinking from there we'll go to Sicily. Please let me know your thoughts on this itinerary and how we can get from place to place (how far between as well).
Many Thanks!

First question is how long of a trip are you thinking about taking?

I think it depends on how much time you will be there and how you will be traveling. Will you be renting a car or relying on public transportation? I think for Sicily a car is your best bet.

My mom and I spent 9 days in Sicily a few years ago-perhaps this will give you some ideas:
http://www.wired2theworld.com/sicily2003.html

Hi, I don't know if this will be of help, but I travel to Italy at least once a year, and I also have several Italian students in NY in my ESL classes. SOme of them tell me that they consider the regional airlines to have become the best and most efficient means of distance travel within Italy herself.
SO if you explore the areas around Bari and want to then tour Sicily, you might explore flights from Bari to Palermo and rent a car there, for example.
WIndjet, AlpiEagle, and Meridiana are three that come to mind. I think they probably have connections between those 2 cities or also from Bari to Catania.
This way would give you more sightseeing time at each end...

We are thinking of about 10-12 days.
The cheapest fares seem to be from NY-Rome but am not sure if it's the best option to fly in and out of Rome...any suggestions?

You will have to change planes somewhere, why not Rome? I flew into Rome and connected to Bari two summers ago with no problem at all. We actually flew on two different airlines, and opted to collect our bags in Rome and recheck them, but it was simple. The domestic terminal where flights to Bari depart is just a short walk away from the Terminal where transatlantic flights get in. You have to go outside, but it's not difficult at all.