If you export all the shapes at one go from mocha and paste them onto only a single layer in AE, the first shape at the top of the effects control panel will have its mode set to Multiply. All instances of the mocha shape below will have their modes set to Add.
If your shapes look fine in mocha then they should look fine, at their default settings in AE.
If you posted a few screen grabs, that may help a lot to finding out what the issue is. If you’re keen to provide screen grabs, then provide the following –
1) layer controls panel in mocha
2) effect controls panel in AE
3) timeline in AE
4) comp panel in AE.
Finally, the best example of a subtraction matte is in the creation of an “O”. You should realize that you will require TWO shapes (or masks if you were to do it in AE) to create an “O”. One shape ti create the outside edge and another for the inside edge. The shape used to create the inside edge is commonly referred to as a subtract or subtraction matte.
In mocha, you can create a subtraction matte in two ways –
1) create a matte in its own layer and set its Blend Mode to Subtract (or Add with the Invert switch set to On)
2) Create two mattes in a single layer where one matte overlaps or overlays over the other.
HTH
RoRK
Intensive mocha & AE Training in Singapore and Other Dangerous Locations
Imagineer Systems (mocha) Certified Instructor
& Adobe After Effects CS6 ACE