Since I'm using AS3 now exclusively, I'll just let y'all know what I've surmised, and anyone can chime in with correction or amplification:
stop(); commands go on the actions layer of
the last frame of a movie clip that's just played in a timeline.
Often though, you'll use gotoAndPlay(); or gotoAndStop(); to send the timeline playhead to a point in the timeline that contains new content (on your images layer, text layer - basically to a "new page" on your timeline). You place the stop(); command on the first frame of these sections on your timeline (btw, these sections could be as little as one frame long,) to give your user a chance to look at the new images, texts, buttons, etc., and decide what he/she wants to click with their mouse.