alpha channel wont help you here, it only puts an alpha for areas where nothing exists. You use this to do things like put a sky in post, etc.
In Blender, you can do this fairly simply.
you will need to have the objects you want on a separate layer. Then the objects you want to form your mas on another layer. In the render tab, go to layers and put the objects to use as masks in the mask layers.
Then I think all you have to do is go to the node editor and plug the alpha channel from your render layer into your composite node.
render the image sequence out in Blender and use that as an alpha layer in your video editing software.
I may have missed something, so if I did, just google it
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