I've done this trip with scouts twice, and you're going to have a great time.
We've stayed at the Inn at Ellis Street and the Doubletree (which I think may've turned into something else? Hilton?). Both were on Bay Street in the historic district. One thing we particularly liked was that both served breakfast (included in the price), and that makes mornings so much easier -- especially with a group. Both had interior hallways, which we considered a "must"; we wanted the girls to be able to run between rooms without going outside. Both had very small pools enclosed in small courtyards, which was a good thing considering we were watching groups of girls. I would have no preference between the two.
I definitely recommend staying in the historic district. Since you're going in summer, parking will be impossible if you don't have a space reserved for you at the hotel. Note that I didn't say difficult, I said impossible, and it's not an exaggeration -- especially if you have multiple cars. There is no parking at the Juliette Lowe House. A hotel within walking distance of City Market will put you in just the right spot for plenty of restaurants, and the ghost tours leave from that area.
The other viable option -- if you want to stay outside the historic area -- is to use a bus and a driver. You can have him drop you off whereever you want to go, then come back for you at the appointed time. However, by the time you've paid for the bus and the driver, you could've had the more convenient hotel in the historic district.
Restaurants:
Lady and Sons -- the leaders like it better than the girls, but it's wonderful! You want the buffet, of course, and you should skip lunch on the day you plan to go! You CAN make reservations for groups, and even for individuals it's not too hard to figure out how to beat that silly system they use.
Casbah Moroccan Rest. -- this was something entirely new for our girls, and they enjoyed it tremendously. We made the evening easy by pre-ordering the chicken kabobs for everyone in the group, and everyone was pleased. They began the meal by pouring water over everyone's hands; that's important because there are no utensils. The food was "different", but not so far outside the girls' comfort zone that they rejected it. A huge hit. We went early, and the belly dancer was very nice to our girls; she got them all up and gave them a lesson.
Pirate House - Ho-hum. The food was average, and the portions were foolishly large (as were the prices). We'd paid in advance, and they weren't interested in giving us good service at all. I would not return.
Blimpy's -- Why would I bother to mention a fast food place? On both trips they've been simply outstanding. They are only about two blocks from the Juliette Lowe Center, and they are well-accustomed to dealing with scout troops. You can order your sandwiches ahead of time, and they'll have them packaged up in a box, each sandwich labeled with the girls' name. They make leading a group very simple. You'll probably do a morning program at the Center, then leave for lunch with the girls, then return for your house tour (or vice versa) -- nothing could be more simple than using Blimpy's.
Activities:
You will absolutley love the Juliette Lowe House. They do it right. Do allow time at the end to present your girls with the Birthplace pin (which can only be worn by scouts who've visited the Birthplace) on the back porch.
Dolphin cruise -- Captain Mike's. You're sure to have a wonderful time.
Tybee Island Marine Science Center -- I'd give this a B. The center itself is nothing; it's barely more than a couple fish tanks, but their programs are very good, and they girls had a great time. The beach, of course, is always a hit for the girls; they have lifeguards on the beach, so you're covered for Safety-Wise. There's a lighthouse, but I haven't done that myself. Parking is fairly easy at Tybee Island.
Ghost walk, historic tours -- These abound in Savannah. The best one we did was a ghost walk, and it was best because we happened to get an incredible host who really knew how to spin a story and kept the girls enthralled the whole time. On our next trip we did a carriage ride /ghost tour, and our host just didn't have "it". It's luck of the draw. There's also a pirate walk that takes place by the river. Some of the companies offer ghost walk patches for scouts.
Wolf Center -- we haven't done this, but I want to!
Travel agents: There are multiple travel agents who handle only scout trips, and we used that route the first time -- we won't do it again. It was very expensive, especially meals. Using them, essentially every meal was $25 (and this was 4 years ago), even if that meal was a kid's chicken fingers plate. With all the advice you can find on the 'net, it's just not worth the extra money.
Mrs. Wilkes Dining Room. 
