Sounds like you're on the right track, but you're also correct that only one mask can be applied to any clip. Two ways to do this come to mind.
The first is to produce the clip with the rectangular mask first, then import the new version and apply the custom mask to that.
The other option is to place a copy of the background clip on track 3 and use your custom mask there, so the masked "background" will be overlaid on top of the main clip on track 2.
Hopefully this montage will help explain what I mean: