We just got back from our WDW trip. There were four of us. We had two of our MYW tickets purchased through Disney which the CRO (through our TA) linked up with our room only reservation. The other two MYW tickets were ones that we received as rewards as part of a product loyalty program (Air Miles).
In the case of the purchased tickets, they were already linked up to our room keys at check in. For the tickets that we got through the Air Miles program, the CMs at the guest services counter at the resort (the Poly) were able to put them on the room keys for us. When we moved to AKL later in the week, they were able to transfer the unused portion of the tickets to our new AKL room keys. Very convenient!