I had a situation like this; having to go to a conference, with me as a FO and my companion not even a SM member. What we ended up having to do was put us on seperate PNRs, so I could be eligable for upgrades. For check-in, she just came in with me and the agent took care of us both in the F/Medallion line, and even though her boarding pass said Zone 8 (mine Zone 2), I just told the gate agent when I boarded that she was with me.

But yes, if you want a shot at the upgrade, make sure you're on seperate PNRs.