The database FMDB saves to is, itself, a SQLite database. You use FMDB to open the SQLite database that is in your Documents folder (which you either copied from bundle or you created programmatically). You never alter the database in the bundle (if you even have one there, at all).
What you will generally do is check to see if the database exists in Documents, and if not, copy it there from the bundle:
NSString *bundlePath = [[NSBundle mainBundle] pathForResource:@"Base" ofType:@"db"];
NSString *documentsFolder = NSSearchPathForDirectoriesInDomains(NSDocumentDirectory, NSUserDomainMask, YES)[0];
NSString *documentsPath = [documentsFolder stringByAppendingPathComponent:@"Base.db"];
NSFileManager *fileManager = [NSFileManager defaultManager];
if (![fileManager fileExistsAtPath:documentsPath]) {
NSError *error;
BOOL success = [fileManager copyItemAtPath:bundlePath toPath:documentsPath error:&error];
NSAssert(success, @"%s: copyItemAtPath error: %@", __FUNCTION__, error);
}
// now FMDB can use the database at `documentsPath`