Getting used to some aspects of Music Creator 6

I'm not sure I understand what you are trying to do. Can you elaborate?
My first guess is that you may be recording stereo tracks that should really be mono.

The panner in a stereo track is actually a balance control. Use the Channel Tools from SONAR 8 for panning stereo tracks.

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.

In reality there are very few instruments that NEED to be stereo.  So set up and record in MONO and your problem should become a non-issue.  Panning a mono track is straightforward.
 
If the track is truly stereo, and needs to be stereo, by definition, and common sense, it needs to be centered so that both the left and right channels of the track are heard. If you pan it, you are losing one half of the material, and in the process of panning it, defeating the entire reason for having a stereo track in the first place.
 
For example, In some of my music I have a true stereo piano and true stereo B3 organs with Leslie cabs that were mic'd in stereo....(when you look at the wave, you can literally see differences in the 2 stereo track waves)  those tracks ALWAYS go straight up the center with the lead vox and the drums and the bass.