You're absolutely right -- that's where Firebird stores the data. Your bookmark files and other settings are actually housed in a deep subdirectory of that folder. You should find all your stuff in ~/Library/Phoenix/Profiles/default/########.slt/ , where ~ is your home folder and the #s are random numbers or letters.
If for some reason you've decided to use actual profiles with Firebird, then the "default" part of the directory will actually be your profile name.