I've been using after effects for about a year and I never really got into the paint tool, I have a few questions about it's limitations and abilities, First of all, if you have a transparent layer, is there a way to paint outside the visible layer and into the transparency grid, there is a checkbox in the effect controls "paint on transparent" that seems to only make a kind of layer reveal effect and not what I'm trying to do.
Second, I was wondering if there is a paint bucket tool, similar to the one in photoshop/Illustrator, and no I don't mean the Effect "Paint bucket" something I could use to color in the frame by frame animation done in the native after effects Layer Tab.
If there is a way to do this or a plugin/script I'd love to know
I'd look at the channels in the paint panel and make sure that you don't only have RGB selected but select RGBA or Alpha. Alpha is painting on the the transparent channel. Also, when you click the brush color I'd look for an eydropper which will let you choose what color on the screen that you'd like to sample.