Blake, I concur with scook.
Assuming you have both programs installed on the same machine, Channel Tools should be available for use in MC6.
I just tried it in MC5. Just insert it in the FX bin of your stereo track.
I suspect that you may have been using the Channel Tools before( in S8), as the "angle" reference is somewhat unique. Standard track panning uses a percentage reference.
For conventional instruments, I record to two mono tracks as spacealf suggests.
However, most soft synths have a stereo output, and the Channel Tools are your ace in the hole.
I don't see that MC5 has the ability to split a stereo track into two mono tracks. I'm guessing that MC6 is the same.
This is essentially what Channel Tools does to allow the left and right channels to be panned independently of each other.