When I compose, I usually begin by sitting quietly and humming or singing out loud until I have a melody that I like. Because I was born and raised in the west, acoustically I'm naturally accustomed to a 12 tone equal temperament.
Atonal music is more difficult for me to grok, and I kind of imagine that for you to be fluent and compose in these sort of microtonal scales you would need to be introduced to it at a young age - in much the same way that it's significantly easier to learn a second language if you grow up in a bilingual environment.