How to place a primer in a pocket is simple, if you have the right tools. Our CPS, with it's mechanical hard stop, can place a primer to within .001 of your desired depth. So you measure the pocket depth, measure the primer thickness from bottom of cup to top of anvil, then bottom of cup to top of cup. That will tell you how thick the primer is, and how far the anvil sticks up above the cup. Subtract the primer thickness from the pocket depth, and you'll be able to see how far below flush you need for proper contact.
You must at minimum ensure that all anvil prongs are sitting on the bottom of the primer pocket. You can completely compress the anvil into the primer, but you risk fracturing the pellet. I prefer .002 to .004 of crush on the anvil.