Do you just set up the ipac to match the keys that are assigned in the emaulator?
Yes
If so, are there default ipac files somewhere set with the defaults for each emulator?
Not that I know of.
Can someone explain to me why and how to configure different ipac configs for each emulator in my cabinet?
how - not without knowing what emulators you are using.
Why - You would do this to accommodate emulators that don't let you re-assign buttons - For example
Emulator A uses "G" as Button 1 and cannot be reconfigured - Simply program the I-PAC with a config file that sets Button 1 to "G" and load it before launching Emulator A.
MAME - Uses L Ctrl as Button 1, but if all you will use is Emulator A and MAME, it is easier to reconfigure MAME to set Button 1 as "G" and not bother re-programming the I-PAC.
Emulator B uses "F" as Button 1 and cannot be reconfigured - Now you have to create a config file for the I-PAC to use it with both Emulators A and B.