I've had to do this quite often and yes, they can link the PNRs, but it never seems to really make a difference if seat assignments get screwed up. Even when I've told them that the mileage tix are for minors...

My advice is to make the booking, call and ask for the linking and the seat assignments, keep an eye on the itins on .bomb, and call back to make sure things are still as they should be a week before the flights.