First put all the cases you loaded in a block with the primers up. Run you finger over the primers to feel which ones are feeling high. Once you identify them, remove the locator pin for the primer position. It is under the die for the powder drop. Now press the handle forward and remove the primer on top of the pin. Once done, you can place each of the rounds in this position and press the handle forward hard. This will finish seating the primers. Do not pull the handle down. You don't want to advance it. You don't have to pull any bullets unless you really want to for some other reason.
Normally when the shell plate is higher than it should be you will get problems with the primers not seating properly. Also when the shell plate is at the proper height it will be more difficult to advance it when you have a high primer. It is something I can feel in the handle.