I did something similar this summer - initial tickets (3x) booked with $ then added another person on same itinerary with an award ticket.
Once the PNRs were linked, I was able to select MCE seats for the award ticket using the web site - no need to call in for that, only to link.
The award ticket did not get free checked bags but we had up to 9 available with original booking, so was not an issue.