You can basically just make the INI include what is under the Execution Settings header.
I made a custom Mamewah recently for a video game tournament where I wanted some Atari 2600 games in with some NES games all in one list. So for each Atari game I made a custom ini.
So my directory structure was like this:
C:\VGT2008\Mamewah\config\skills
This had the normal ini, layout file, background image etc...
C:\VGT2008\Mamewah\config\skills\game
this had (among others) dragster.ini
### dragster.ini (mamewah v1.62) ###
### Execution Settings ###
pre_emulator_app_commandlines
emulator_commandline [emurootpath]\Stella-1.4.1\stella.exe "[emurootpath]\stella-1.4.1\roms\[name].bin"{dosbox}{safelaunch}
post_emulator_app_commandlines
So by default, the games will run in the nes emulator, then if theres an INI file in the game subdirectory with the same name as the rom file selected, it would execute what is written there, in this case, stella, and the path to the atari rom.
Hope that helps.