Yeah, you'd only want to use multimame if you want mala to see 2 version of mame as just a single emulator. For instance, if you're running a stable version of mame that you generally like but one particular game doesn't work in it, you can use multimame to run a separate version of mame for that one game, but mala doesn't even realize that you're using 2 versions of mame.
As to what you're trying to accomplish, I'm curious why you want them to be seen as separate emulators? Is it for the type of scenario Ummon describes, running a variant like misfitmame? Personally I like all arcade games seen as one emulator. I combine mame and daphne, so if I were to run a variant like misfitmame I'd include it in there too.