I need to run a live camera with an animated border around it. My problem is, some of the moving units pass over my transparent area, and I need for the transparent area to show the video uninterrupted. Is there a way to make a layer on top of the lower layers that will make everything below it transparent?
Unfortunately I have no idea what your shot looks like or what your requirements are from your explanation. A border with transparency placed on the top layer will show everything below it. If that is all you want then you need a compatible source for the border video with an alpha channel to feed into some kind of switcher for your live camera can have an overlay.
If you are not using a "live" camera but are building your shot in After Effects or PPro then the same technique applies.
If I am not getting it and please provide a screenshot or a storyboard and a detailed explanation of exactly what is happening in the frame so we can help.