mike boss,
I don't have the answers to all your questions, but I think I can tell you what batch files are perhaps.
A batch file is essentially a very small program that will execute simple computer/command line style commands. Google it for a better description. Most often used for repetitive commands used often for on many many files. Works well on many many "rom" files sometimes.
Batch files are not required with Mala but sometimes it's easier to set up certain things within an emulator or launch and emulator outright when using a batch file.
For example, I use a batch file to launch each of my Daphne (laserdisc emulator) games. Why? Because it really hard to launch and pass the correct info to Daphne to launch a game using a command line structure out of Mala. So I point Mala to a batch file for each game and the batch file launches Daphne with the correct info for each game.
I've used batch files to auto copy and paste files for other emulators. Demul for example cannot be configured to switch bioses or control configurations for each game and have those settings be saved. Since it cannot be saved for each game, I do some quick copy and pasting of .ini files when launching each game from Mala using a batch files.
Each emulator is different. Batch files can help fill in the gaps where Mala or the emulator itself aren't helping.
I hope this helps.