EPT1) It always optimizes for time. So if say you want X roaches, the build you get back is the one that got X roaches the earliest. If you had a time limit, then it either tells you how much it beat it by (if it succeeds) or how far along you are at the deadline (if it failed).
2) You have to use the waypoints to force a build order. It's pretty annoying because the waypoints care about when stuff finishes instead of when it starts, but it can be done. Try telling it you want 2 overlords by whenever a 9 overlord pops (waypoint 1), then 14 drones at the appropriate time (wp 2), then a spawning pool by 3:05 (wp 3), then some arbitrarily high number of drones in the "target" tab... that should work.
I didn't particularly trust it after tinkering with it... I don't think a genetic algorithm is really the best approach to this. I'm not saying don't bother, but don't treat its results as the last word on the issue.
