I chuck the countersink into a drill and remove a bit of material by feel. It isn't scientific by any stretch, but the primers seem to go in just fine, and no leaking yet (not pushing max loads and using Wolf "milspec" primers). Sometimes I have just a tad more difficulty seating a primer than with some of the processed brass I bought from gibrass.com but on the flip side the "chamfer" edge guides the primers in much nicer on my Pro1000 press.
If you don't want to use a countersink Hornady makes a primer reamer just for removing the crimp. http://www.midwayusa.com/product/253...ter-head-small
If I had a drill press handy that would probably be the tool I chose. Mount a wood block, drill a brass recess in it, and then process brass as quick as I can swap brass and work the press.