That’s pretty clever. If you’re writing with the Wacom tablet in photoshop you could make your background white and the brush black and then when you bring it into AE set it to multiply mode and it will knock out the white BG. Also, you could use the invert effect to flip the black and white and set it to screen mode. OR use the free Knoll UnMult plug-in, which will remove the black without having to blend with the background layers. Just stick the invert effect in front of the UnMult effect if you need to flip the colors.
One word of warning though, is that you may run into some weird behavior or bugginess in AE if you use a highly compressed video format, which most screen capture apps do use. I would bring the movie into AE, precomp it and set the size so it crops out the parts you don’t need, then render to a quicktime animation or PNG sequence and use that in your project and not the compressed format.