I am in Denver now, having done the same thing. IAH-DEN on a CO flight, and UA on the return (as a codeshare with a CO flight number). I am CO Plat, matched to Prem Exec.

I made the reservations on CO.com with just my Onepass number and I was upgraded on both flights. Five days out on the CO flt (earliest possible but no email notification) and three days out on the UA flight (no notification at all on CO, it still shows Economy, but on the UA side it shows Upgrade:confirmed. I had to call UA to give me a seat assignment, though, neither site allows me to do that).

Every time I have done one of these the procedure seems to change, but at least it always works in the end. I guess there would be an advantage to use the UA number because it would have placed me in front of those Plats that have not matched, but now that many people have matched I don't think it makes much of a difference.

I also want all of my miles on the CO side, but I suppose in the end that won't matter either.

Followup: I was upgraded on the DEN-IAH UA flight and had the seat that was assigned to me over the phone. Both CO.com and UA.bomb continued to show me in economy with an economy seat 7C although UA showed Upgrade:Confirmed.

When I checked in online, it gave me a message about my upgrade, had the seat assignment correct and issued me a boarding pass with the UA flight number. The BP had my Onepass number, but my status was only "*Gold". It really didn't matter since I was in FC, though.

So, at least this time, everything worked out well, but certainly the systems could be integrated a little better.