I wonder how I would make my own mega man x song like in the first three snes games. Can anyone help me with the looping and how to actually use milky tracker and the sample settings required in general for the instruments?
You haven't come to the right place to ask about XM samples. This place is about Famitracker, a NES/Famicom tracker that does not deal with PCM samples of the kind you are looking for.
go to the sample editor on milkytracker, theres a loop option on there with a few selections, choose forward and mess around with it until it sustains right.