When flying a partner, I always give them my preferred airline number when I make the reservation and then confirm at check-in that it is actually in the record.
Whenever possible when looking at AS partners, I try to fly NWA or AA because their miles (plus their 1st class bonus miles) count toward AS status whereas those of TWA or CO do not.
I also always maintain my ticket stub and record containing the actual ticket number the mileage has actually posted.