My preferred method is to have written something already on another instrument, either guitar or keys, and then just transcribe the notes into the tracker. Once that's done, it's just a matter of adding drums and other accompaniment, and tweaking the effects column to achieve the desired... effect.
I'm not very prolific with fully written instrumentals though, so sometimes I recall one of my many gay pop songs that I never finished, and I'll try to transcribe it into the tracker, turning the vocal melody into the main instrumental melody. That can be a problem because some melodies that work as vocals don't translate very well into pure instrumentals. It's easier to get away with repeating the same note when there are words attached to it than it is when it's just an instrumental tone.
So usually I end up just fucking around with a 4 or 8 bar loop, just kind of improvising and adding a bunch of stuff, and then building the song out of that loop, for the most part. It's either completely melodic and in a single key, or I deliberately make it math-y and move all the notes around according to certain intervals, like minor thirds or something, and then try to somehow find a melody that traverses several keys within 8 bars.
I find it difficult to really develop these kinds of loop-songs beyond just muting and un-muting the original patterns, but on the other hand, they are always spontaneous and fun to make. Also, on a good day, I can crap out a whole bunch of these things and at least feel productive, even when they all suck.
