I found a way around this. After I applied the first mask, I right clicked and chose Nest to nest the clip, basically making the first mask baked in and then I could apply a second mask and control it independently. However I could no longer adjust the first mask. So I found that if you only make masks after you apply the Nest, Premiere creates separate sequences and you can go into each one and still edit each mask, so just dont apply any masks until after you nest. You can nest multiple times also. This allowed me to mask and even use the invert tool multiple times and still go back and change each mask as needed.