Next he'll take his sample (already timestretched to the tempo of the highhats) and paste that onto a track in the multitrack view of FL Studio under the highhats. He'll open that wav file loop onto a track in the multitrack view of Cool Edit Pro and loop it out for a few bars. The way Flash (and I'm assuming 9th) does it, is he'll export a loop of highhats hitting on eighth notes from FL Studio to a wav file. I believe 9th showed Flash how to sample and if their methodolgy is the same, then it's a good guess that 9th doesn't actually do his sample chopping in FL Studio.
Now I can't say for certain this is the way 9th Wonder samples, but one of my friends is DJ Flash.DJ for Little Brother, Justus Leauge, and one of 9th's friends.