I had problems in Taipei back in January where the agent checking me in for an EVA flight didn't want to enter my OnePass number (I didn't have a OnePass account when the flight was booked; I signed up specifically for that trip so that the miles would eventually combine with my Mileage Plus account). The agent in LAX
on my outbound flight didn't have any issues entering it, and sure enough the outbound flight appeared normally but I had to send a copy of the boarding pass to Continental to have the miles credited for the return.
I just booked a flight with China Airlines last night, and they didn't have a space to enter a partner frequent flyer number (only Dynasty Flyer numbers). I called the CI
reservations center today and the agent added my SkyMiles number to the reservation.
I don't have any specific experiences with Air China, but as a Star Alliance member you should be able to receive Mileage Plus credit, unless you were booked in the booking classes that don't earn miles (probably these are mostly free/award classes and possibly consolidator classes, but I'm not sure). If you don't receive credit or the CA
agents refuse to enter your MP
number, you will want to send documentation to United after the fact to earn credit. Instructions are on their web site. You might have better luck with US-based Air China employees, as they're probably more used to dealing with Mileage Plus issues than their China-based counterparts.
As a general strategy, you want to keep your miles consolidated in as few programs as possible since it's quicker to get enough miles for an award that way -- and with alliances, partner flights can qualify towards elite status. So it's pretty rare that you'd need more than one program per alliance. My Dividend Miles account sits nearly unused with very few miles in it; by the time I flew US with any regularity they were a Star Alliance member so I had all those miles credited to my more active Mileage Plus account.