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You've just about answered your own question.
In AE - you'll use a TRACK MATTE. It requires the fill layer to be "under" the mask layer.
You'll create two separate layers of video. The lower one can use the luminance or alpha properties of the layer above it to define transparency.
This way, both can be animated separately.
There are several resources for techniques. "Track Matte" is what you're looking for. (in the switches and modes column)
Thank you for your help! I looked up track matte in the help menu and I tried making a solid shape layer the size that I want my mask to be and put it over the layer I want masked. None of the track matte options in the timeline gave me the result I wanted which was allowing the bottom layer to show through only that shape. The other problem is I cant figure out how to make my solid have feathered edges. What am I doing wrong? Thanks!
You can either BLUR the top (mask) layer, or add a Layer Style (glow) to soften that edge. If you're using a mask shape (not primitive shape), you can use mask Feather.