Can anyone advise of the best areas to stay in these cities.
We will be driving but prefer to explore on foot or public transit so like central locations or near transit stops.

At the early planning stage so just looking for general guidance please or if anyone knows of useful websites.

Thanks

Savannah and Charleston are very walkable cities. Atlanta not so much. But MARTA gets you several places of interest.
What are your interests? And are you talking hotels or AirBnB or combo?
Charleston anywhere in historic city center area. Same for Savannah. Though we stayed across the river at the Westin and just took the ferry across.
Downtown Atlanta has a lot of interesting things to do during the day, but not so much at night. You will probably end up driving more there.
Also both Charleston and Savannah have interesting oceanfront parks close by.

Mills House is my favorite hotel in Charleston. Easily within walking distance of most major attractions. You'll have to drive to visit the Battleship, but it's worth it.

Okay, now that I am in front of a computer, a bit more advice.

1. Between Atlanta and Savannah is Warner Robbins Air Force base. They have an excellent aviation museum there if you are interesting in that. https://museumofaviation.org/
2. Charleston - across the river is Patriot's Point with an aircraft carrier and the WWII destroyer USS Laffey. I think Folley's beach is worth the drive. Quaint little beach town and parks and lighthouse. In North Charleston there is the Hunley submarine from the Civil War.
3. Take walking tours of both Charleston and Savannah.
4. Do the Pirate House or the Pink House in Savannah. Yes, touristy, but historical as well.
5. In Atlanta, I would recommend a visit to the Ponce City Market, but you will need to drive. https://poncecitymarket.com/ . There is so much to see and do in Atlanta, but driving is almost always required. You could stay near a MARTA station, but not sure how helpful that would be. You can get to/from Buckhead, downtown, Decatur, but even then most areas require walking significant distances.

In Charleston, we stayed on Cannon St in an AirBnB complex. About a mile and a half walk to the furthest historical sites. But you are walking down interesting streets with lots of shops, restaurants, and places to refresh.
In Savannah, we also stayed at the River Street Inn, right on the river. Note, if you take the haunted Savannah tour and your spouse doesn't like ghosts, it does not help that one of the stops on the tour is the hotel you are staying at. Soooooo, we won't be staying there again.

when matters.

what interests do you have?

if you are a golf fan you have the masters course in Augusta, GA. The tournament is in early April so hoteks will be expensive then

do you want to explore the coastal area beyond the cities? Hilton head is just over the border from Savannah. South of Savannah you have a bunch of coastal areas to explore.

Hilton Head Island is a nice barrier island north of Savannah and south of Charleston. The beaches and marshes are very nice. It would be a nice stop over on the way from Savannah to Charleston.

The tourist areas of all three cities are quite small and very walkable. Savannah about 1 square mile back from River Street, Charleston a bit bigger but it has a good tourist bus system, Atlanta downtown small but the suburbs are huge. A strategy of find the closest Holiday Inn Express that has free parking would work for all, though stay off the roads at rush hour, or pay the higher price and stay right in the middle of the tourist areas. Driving on the interstates between the cities is very boring but there are some very nice attractions just off the interstates if you want them. Any state park, and there are a lot of them, will be a nice spot for a few hours. There are also good beaches on the coast and good Civil War attractions near Atlanta. Kennesaw Mountain is one of my favorites.

Hilton Head Island is wonderful if you're looking for golf, tennis, or just somewhere quiet to relax.

Charleston is extremely walkable. We love the downtown area. Patriots Points and the battleship are good for a full day visit. Rush hour traffic can rival ATL/MIA for congestion. James Island County Park is excellent with hiking, walking, and paddle boats. If you're into golf, Charleston Municipal is phenomenal.

Savannah is not my favorite city in the southeast, but it has its charm. We did a horse carriage history tour which we found extremely interesting. The River Walk is fun if big ships are coming by, otherwise it's touristy and full of trinket shops and sweatshirts.

Yeah, if you are deciding on number of days, spend more in Charleston than Savannah. And that is one reason we liked staying across the river at the Westin, watching the big ships go by. You could literally cover Savannah in a day and evening and be done. But do a walking tour for sure. Charleston has many more sights, history and great places to eat/drink/shop.
Atlanta - I do like Stone mountain - tram to the top and hike down if you are into that. The evening laser show is interesting.
Off the beaten path stops: Oakland Cemetery with several famous people interred there(bring a golf ball). Have a drink at 6 Feet Under bar across the street. One Flew South is a highly regarded nearby restaurant (of ATL Concourse E fame). The Krog Street tunnel painted walls and nearby mural projects and Cabbagetown in general is interesting. https://cabbagetown.com/

Let us know your interests and folks can probably give more specific advice.

Thank for all your replies it�s a big help planning.

not going until May so still at early stages.

later in May the hotter it will get.

atvthus time of year you are going to encounter high school and college graduations. College town hotel rates are going to be high if timing hits graduation.