Yep, did the same thing. It has been a while back now since I went to the LoadMaster in order to get more turret positions. I am trying to jog my memory how I did it.
Due to Lee's crappy priming system, I decapped/sized all my pistol brass in one run thru the press. Then, I would hand prime. After that, the business began. My Pro1000 was only a 3-hole turret job, so I charged in station 1, placed a bullet by hand in station 2 and seated, then used the FCD in station 3. The way I did it, you could still use the case feeder.
You will need the Lee spacer/extension tube to raise the Pro Auto Disk over the other dies to prevent any interference with the powder drop mechanism.
ETA:
You won't get the bullet feeder in the system the way you want it to be, To use the FCD, you will have to place the bullet by hand unless you have a Pro1000 with the 4 turret set up.
If you want more processes done in a single stroke, you will have to upgrade to a press with more turret holes. I use a LoadMaster, but I should have gone Hornady at least. Dillon is the go to for more and better mechanizing the process.