Well... if it was really important to keep them independent, you could make one layer your footage, and another layer a Track Matte. If you don't know what a track matte is, it's basically a video track that defines the opacity levels of another video track. The original video layer looks at the level of black and white in the track matte layer and thats how it defines what is opaque. For example, if your track matte layer was just a white rectangle on a black background, then your video layer would only show through that rectangle area.
Now how this applies to what you're wanting to do is slightly complicated, but can be done. it'll involve making 2 compilations. 1 compilation is the track matte, the 2nd compilation is the original video, plus the 1st composition as its own layer. you'll make the track matte composition as a series of masks. If you're doing your masking in Photoshop, then you'll want to just make your mask black and white (a solid white shape around what you want masked, and everything else black), then import it into AE, and just line them up. Because each image is its own layer, you'll basically just have to kind of "stack them" one by one, moving each frame over, but it can be done.
Once the track matte comp is done, you put it on top of the original layer in it's own composition, then set the TrkMat property on the video layer (if you don't see it on the main timeline window next to the video's name, click the Toggle Switches/Modes button at the bottom and it should show it), and set the Alpha Matte to the new track matte composition you made.
Heh, if this all sounds too complicated, its because it kind of is. you're really better off just having individual masks on the video layer itself
