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All tracking in After Effects uses a feature region and an attach point. You can track as many individual features (the inside square) as you like and attach as many reference layers or nulls as you like. You can also track surfaces in Mocha Pro.
Stop motion photography requires you to have prominent nonmoving features lined up or to use carefully planned camera moves and then manipulate the objects in the scene that you want to move. I'm not sure how Motion Tracking is going to work unless you have some surfaces that you want to lock in place to fix some poor camera work.
It would really help if we saw that scene you were working on. I'm imagining a model railroad set with three surfaces you could track.
If you track all of these objects on a single layer in Mocha AE and then use the transform instead of corner pin the 3 objects will stray lined up, but if the camera is moving then the parallax between other objects in the scene is going to change and look very odd.
Show us your scene and we can give you a much better idea of how to handle the post-production problem you are running into.
Thank you for the reply. I have several photos like this from different locations and I would like to align the shots with the camera. I did it one time, you can check the video here - https://www.instagram.com/p/BwpcOa_AQLP/ but I was just wondering if there is a way to simplify this process. I made this in photoshop and it's not very accurate.
No, no ... I didn't want to make all the work by software. I just wanted to go pic by pic and manually choose 3 same points on camera. For example, some buttons and then make the software to align those points.
On this pic, you can see how I tried to stabilize it, but there is still some wiggling, which 3rd point maybe can fix.
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