If I understand what you are asking, what you are trying to do is fairly simple, however it would be a lot to explain through a forum post. Basically what you want to do is connect your tracking to a matte of the eyes and then use that matte as the alpha for your video.
To do this, apply your tracking data to a new solid, (or better yet a null object and then parent it to a new solid). Then use the pen tool to cut out the shape of the eyes onto your new solid. To do this you will have to lower the opacity or turn off the visibility of your solid so you can trace the shape of the eyes. Either way, make sure the solid is selected while creating your mask. Create a separate mask for each eye and then set the solid opacity back up to 100% if you changed it. Next, place your solid layer directly about your eyes video layer. In the video layer’s TrkMat (Track Matte) column, select alpha matte. Your eyes will now be the only thing visible. You will most likely have to animate the mask shape of your two eyes so that they stay lined up with the eyes of your talent.
Now I have oversimplified this post to keep it from being way too long, but I have simplified parts where you may need more instruction. I suggest taking a look at these tutorials:
After Effects Basics tutorial on Motion Tracking: https://goo.gl/pHUsF
And another Video Copilot tutorial called Eye Replacement: https://goo.gl/oSKGX
These should help you out and go into much more detail then I am able to here.
Jesse Toula
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