

Show us your timeline and explain your design goal in detail and we can give you more precise instructions. Your original workflow of rendering a layer and then tracking the rendered layer that now has transparency, then rendering again suggest to me that you could have just selected multiple splines (Layers) in Mocha and rendered a layer for a track matte to poke multiple holes in a single layer.

The exact workflow depends on the things you need to accomplish. I also rendered black and white mattes to use as Track Mattes. Having a bunch of masks on the Mocha layer does not affect anything if they are all set to off. I created a bunch of masks on the layer that had Mocha applied then just copied and pasted them, or in a couple of cases used expressions to mimic the mask shapes on other layers.
