Is there any key for when to click the bobber? I know you have to click it after it bobs, but does it work better to click immediately or wait a little bit? I always try to work out theories but I'm probably just imagining it.

Doesn't matter. It just has to be within 3-4 seconds after the bobber shakes. If you keep missing things, its just because your skill isn't very high for that area, so either keep trying or move somewhere a lower level :P