Your workflow has more twists and turns than a bag of curly fries! 😉
You have multiple issues as a result of having to track a region(s) with occasional occlusion(s).
Forget about Adjustment Layers for this task. Unless you are using a script that tracks mask, you should only apply one mask onto one adjustment layer – NO to multiple masks on a single Adjustment Layer.
If your tracking region gets occluded, by a foreground object, then switch to Offset Tracking. You initiate Offset Tracking in AE by ALT+dragging the Search and Feature regions onto an area that is identical, relative to the inherent movement of the original tracking region and the camera’s movement.
When ALT+dragging the Search and Feature regions, ensure that you DO NOT move the Attach Point from the original tracking region.
Lastly, you should be looking at using mochaAE/mocha Pro. mocha has the advantage of tracking multiple regions at one go. You can also first track a Holdout Matte, the foreground object (character) that occludes your multiple tracking regions, and then use this Holdout Matte (track it only once), multiple times for each of your actual/desired tracking regions.
Let us know if you have more Qs, but please do as much work on your end first as it seems that there is a lot of RTFM that is required on your part.
Cheers
RoRK
Intensive mocha & AE Training in Singapore and Other Dangerous Locations
Imagineer Systems (mocha) Certified Instructor
& Adobe After Effects CS6 ACE/ACI