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All my favorite downtown restaurants have been mentioned and I also wholeheartedly agree with the bed and breakfast idea. If you stay downtown, you can go for a romantic horse and carriage ride, walk around Waterfront Park, go on one of the Ghost Tours (October!), shop on King Street, browse the Market and walk the Battery, see a play at the Dock Street Theater, and the list goes on....
Two Meeting Streeet Inn is a fantastic bed and breakfast which is in walking distance to so much...great choice! You can also Google Bed and Breakfasts in Charleston to find other options and price ranges.
Kiawah and Seabrook are very nice (I live out in that direction), but very far from everything which would give you the true feel for Charleston (other than Angel Oak on Johns Island).