You can use 2 masks in AE. Just adjust the paths. I'll have to check on exporting the feathered mask from Mocha AE. I know you can from Mocha Pro.
Edit: Turns out all you have to do is select Export Shape Data from Mocha AE, Copy to Clipboard, then paste to a any layer to get that feathered mask into AE. The shape can then be used as a track matte or may be applied directly to the footage.