Please be careful of double posting, since this post could really have been an edit to your last one. Anyway...
Afraid I've only used EonTimer, but I'd image the principles are the same: In general you'd press A after/on the final beep (i.e. when the timer goes to 0). If that's messing you up though, ignore the beeps (or turn them off if there's an option) and go by when the timer ends. Honestly, it doesn't really matter what you do as long as you do it consistently. On that note, you have to be accurate to 1/60th of a second iirc, so you're bound to mess up a lot and be slightly off each time. Keep at it and you'll hit your seed eventually.
Welcome to Smogon btw! ^_^