What is the consensus on which FF # we should use for maximum benefit when flying on CO.

Since CO joined *Alliance, I have always used by UA FF#, but I noticed today when checking in to fly EWR-HKG on CO that our company travel agency had automatically entered my CO number. By default i changed it back to my UA number but after i had done that I wondering whether I was missing out on bonus miles or somehow missout on UGS "credit" if i am flying flights where my FF# is not matched up with the carrier i am flying on since they are supposed combine eventually and use combined UA / CO revenue for 2012 GS.

Any thoughts.

Thanks
TMAYER