Thanks Darby and Roland.
I have a follow up question. I have two seperate passes of the exact same footage, one photoreal RGB, and one Alpha to mask out selected items. Why is it–and this is just my guess being new to AE; that when you use the 3D camera to track footage, when I bring in the alpha to matte, nothing is lined up anymore? Frame for frame, everything is off. How do I go about getting that done correctly? Or am I implementing a terrible workflow? I have attached an RGB image:

Basically, I have text that follows HVAC ducts as you orbit the scene, and I thought I would be able to highlight/make each system (HVAC and electrical) glow as that texts appears by using the alpha channel as a mask/track matte. Is that not possible?