Sorry, but I don't quite get the picture.
I have never played with loop creation so I may be in the wrong ball park here, as I don't even know if there is such a thing as multi-track loop that you can import into a player/loop editor.
Maybe what is required (or would be the easy way out) is bouncing the tracks to one audio clip to be edited in a loop editor and used as any standard loop?
I assume what you're after is not just looping the tracks?
"Hidden tracks/hiding tracks" could have something to do with your "phantom tracks".
I agree with Jonesey that it's relatively fearless to accept deadlines before learning your tools first.