Ciao Courtney,
Sorry for the delay, lots of new questions posted in the last few weeks and I'm sorting through all of them to get them all answered!
Yes, I think Florence would work better as a base in general seeing as you're interested in organized tours (have you booked any?) or train travel and you're going back to Rome at the end, so catching a train from here would just be easier.
Let's start with the questions about train travel: you're going to be within the region, so all trains you catch will be regional, without seats assigned. The easiest and cheapest solution is to buy tickets once you're here and right before you go on your day trip. There are automatic machines in Florence's SMN train station and you can buy round trip tickets then, even if you don't know what time you're heading back. The reason is this: tickets are just for a type of train and between destinations (you pay based on km) and you can use them anytime within the following two months after purchase. The important thing is this: before you get on the trains, make sure to put the tickets in the yellow boxes found at the start of the tracks to "stamp" the date and time on them - you need that stamp on the ticket when the controller comes around and asks for your ticket!! Don't get on the train without it, as you can get fines if you're caught with a ticket but no stamp (they'll think you're trying to use it more than one time).
So pay by day, stops are very easy because they are announced over the loudspeaker and you see large signs with the train station names on them as you approach the station and the train slows down. Pisa, Lucca, Siena, San Gimignano are within an hour train ride from Florence.
Train to Rome might be the most expensive because there you can take a faster train - which means costs more. That is up to you, it is the only one you might wish to purchase online now if you see a special offer on the train's website... the fast trains do assign seating so if you have a particular time by which you need to be back in Rome, you might want a particular train and for that reason alone you might book ahead. For all trains, the website is
www.trenitalia.com.
Now on to accommodations: I can recommend several B&Bs in Florence that fall within your budget for the 5 nights and which you'll love. I know the owners and thus can assure you will have a great stay there. Take a look at these B&Bs:
Casa dei Tintori
Le Stanze di Santa Croce
Residenza Casanuova
This is more like a small hotel:
Antica Dimora Johlea but it has several locations, so you have more choice... and finally, this small family-owned and managed 4 hotel with reasonable rates:
Hotel Principe
Are you interested in having a small apartment with kitchenette while here? those are really popular too, if you think you'd prefer the kitchen... but it is a completely different experience than staying at a B&B. For instance, see the ones at
Palazzo La Medicea