Literally the only time you need to care about the difference between midi and mus is for vanilla doom modding (for DOS or Chocolate Doom). Every other port supports midi format.
If you really want to make a VANILLA DOOM compatible mod (note: there are a ton of rather cryptic limitations you will have to deal with that you don't have in (g)zdoom/zandronum), here's how you'd use midi2mus:
midi2mus is a command line application, you have to put the midi in the same folder as midi2mus, right click on the folder where midi2mus is, click "open command window here", in the command prompt that pops up, type midi2mus and you'll get directions on how to use it.
I don't remember the exact syntax but it's probably something like midi2mus mymidifile.mid mymusfile.mus