Brain isn't functioning this morning. Is it possible to use the align palette with multiple masks on the same layer?
Trying to center a couple circle masks...
No. Try copying the path, pasting in Illustrator, then align, then past back into AE.
The other option is to use shape layers. You can numerically align them or make each shape a separate layer and align them with the alignment tools.
You could also put each mask on a separate layer, align the layers, then copy and paste the masks back to a single layer.