This is fairly simple to do.
For each emulator you use, you create a cfg file that contains the button assignments you want. One thing to note is that you want to avoid the alt key for any configurations, since that can cause some undesired effects (especially if you have 2 players) when pressed in combination with certain keys.
Not much else to say here. You set the program you want to use to flash the ipac and make sure it has %config% to load the .cfg you specify under the details of each emulator set up in Mala.
If you want a seemless experience, (where no windows borders show), most emulators can start out maximized, and you can also set up a hotkey for the emulator in MALA that specifies to use an ALT-F4 when you press the ESC key (or whatever key you decide for exiting the emulator).
I've done this with NES, SNES, ATARI, GENESIS, and several others. Mala documentation talks about this in some detail.