If I interpret your post correctly:
The only die you initially set up to touch the shell holder is the SIZING die. You DO NOT begin with the SEATING die touching the shell holder. Set the SEATING die up as follows: Put a case in the shell holder and raise the ram all the way to top of stroke. Then, WITH AN EMPTY CASE IN THE SHELL HOLDER, screw the SEATER die down until it makes contact with the mouth of the case. Do not force it any further. Now back the die out about 2 rds and lock the lock ring. Then when ready to seat a bullet, back the seating STEM out of the die a LOT. Charge a case, insert it in the shell holder and place a bullet on top. Raise the ram to top of stroke again and screw the seating stem back down until it touches the bullet. Lower the ram slightly and screw the seater stem down some more through trial and error until it seats the bullet to your desired depth. Lock the seater stem down.
If I have mis-interpreted your post please forgive my error.