The Lee 1000 is the three holer right? If it where me, I would Deprime, Prime, and Size on a single stage in one operation. Then run Powder, Bullet Seat, and FCD (if running a Semi Auto) in the 1000 simply to avoid the 1000's big problem, primer feeding.
I would then just lube cases like I would when loading single stage, put in plastic ziplock bag or plastic container with lid, spray a bunch of Hornady One Shot in it, shake the cases about and make sure they are all lubed up, open the lid on the container or unlock the ziplock and let them "dry" then run them through the FL sizer. Thankfully I pretty much only neck size brass, but for a SA that isn't possible.
I've thought about doing something similar with reloading .45ACP, buying a Lee P1000 and doing Full Size/Deprime and Prime on my Anniversary Single Stage where I can get around the P1000's major fault.