Re: Seating primers
You're sort of focused on the wrong end here; the bottom of the primer's the important part. Take care of that, and the base of the cup will take care of itself.
You need to make sure that the primer is fully seated in the primer pocket, with the anvils flat within the pocket. You want a bit of a "pre-load" on the compound, slightly crushing it to sensitize it properly. Do this, and you'll find that the cup is now seated several thousandths below the case head in a properly dimensioned case. In practice, I usually wind up holding the case inverted, between my thumb and middle finger, and drawing my index finger across the now seated primer. You should be able to discern a noticeable "dip" as the finger passes over it. Given just a bit of expereince with this, you'll develop a thoroughly educated sense of touch that will tell you that the primer is seated correctly, or in need of some extra attention.
What you really want to avoid, especially if you're loading for a semi-auto, is any sort of primer protrusion above the case head. Misfires at best, slam fires at worst, and a host of other problems in between those extremes should you fail on this account. Check 'em, make sure they're below the case head and well bottomed within the pocket. Do that, and you're good to go!