I just went through this! I bought a room/ticket package from Run Disney. But, after contacting the Run Disney Mom on the Mom's Panel, I got word that I needed to call Run Disney and change the way it was booked. I called and said that I wanted to "separate my room reservation from my ticket reservation" and it took a few minutes, then I was done. I received my plastic tickets in the mail about a week later, then linked them myself by typing in the numbers into my
MDE account online. It worked perfectly.
If you do this, you can book your FP plus reservations 60 days in advanced. Let me know if you have any questions about this -- I have been researching this for a while and finally figured it out