From talking to some folks at the technology forum, they told me the issue with multi-carrier itins reflecting mileage should be gone. It's kind of fixed.

I have a trip next week on UA and CO. I have a flight on UA from SAN-SFO and then a flight on SFO-EWR a few days later. When I pull it up online, the United flight shows "500" in the miles column. However, now it has no elite percentage listed so that's a step in the right direction.

My other issue is that I went to co.com to change the CO leg and it failed and just told me to call the support desk. So, it appears that the UA leg is preventing co.com from changing the co portion.