Handling Brackets, going from pools into the final bracket

At larger tournarments where you have pools, if I understand it correctly the top two from each pool (the victor from winners finals and losers finals) move on to the final bracket. From there I’m a bit lost. Can you still use challonge to run the final bracket and how do you separate those who are on the winners side from losers, or is there a better tool than challonge?

AFAIK, no there isn’t. You simply state ahead of time how many pools there are, and assign pool seeding ahead of time.

For example, you have 4 total pools. Pool A, B, C, D. So you’ll have a total of 4 players in winner’s side and 4 player’s in loser’s side. You can set it so that A plays D, B players C, or any combination therein.