There's a conglomeration of decent motels on I-95, 15 minutes from the heart of town. (I was told it's a popular stopping point for people driving from Miami to NY.)
Last time we went to Savannah we picked up a motel guide from the lobby of Shoney's, and walked into a place without a reservation. (Don't remember where we ended up, but the guide offered great rates for walk-ins .) The rate was incredibly low, included breakfast -- and unlikesome better hotels in Savannah, there was a pool, which was relaxing at day's end.
We drove into town every day, and never had a problem finding parking. If you're making a special trip, I don't necessarily recommend going without a reservation -- but in researching places online, check out the area outside of town, off the highway.
Went to Savannah last year. The absolute best way to book is priceline and bid on the hotel yourself. You can pretty much know what you are getting by going to betterbidding.com and looking at Savannah, GA and find out which hotels are in which areas and what star level they are. I think we got a 5 star for like 80 dollars. WELL worth it because the town is so small too.