Those will already be set as part of the game entry.
For instance, say you want to play a game that requires NTSC to run. You highlight the game in the database and click on the entry. Before loading the game, Gamebase will replace the ntsc=False line in the Gamebase.uae to ntsc=True. Same thing goes for other critical settings. You can also set gamebase up to detect how many floppy drives to enable based on how many floppies make up the game. Up to 4 of course. If a game will not run with more than one floppy enabled that can be set as well.
Now, this may not be obvious to those that have looked at gamebase but there are many things you can do with the G.E.M.U.S. scripting language.