I wrote this to help people like you get started:
http://forum.arcadecontrols.com/index.php?topic=56010.0It details how I configured all my emulators a while back. You should understand how to associated layout files with emulators pretty easily by going to the correct section and reading quickly about it.
As for my PC games (which are not described in that document), I simply created a BAT file for each of my installed PC games. I then placed all of these BAT files into a "PC Games" directory. Finally, I configured MALA with a new "PC Games" emulator and pointed it to the "PC Games" directory and set MALA up to use only "BAT" file extensions for this new emulator. What this does is tell MALA that a new "PC Games" emulator exists and to treat all files ending in "BAT" to be the game names. Once you start MALA, you should be able to scroll through the BAT file names and select one, which will result in the BAT file executing, thus starting your PC game.
It has been a long time ago since I set all of this up, but it was pretty straightforward and worked well. I would suggest you open up another forum post regarding how to set up MALA for PC games and here what other people recommend as well ..... but what I told you should get you going ....