Lots of how to write ups on the net, and this video:
http://www.youtube.com/watch?v=jUol4R9nYAw
I wish I had watched this before I tried my first PTO removal. That style of hex wrench is the way to go, hammering it in is mandatory. The back and forth motion (driving the set screw back in when you hit a stop) goes against your nature to keep that thing backing out, but it will save you. Two set screws per hole, TAKE YOUR TIME.
You do not want to be in the position of drilling these out. Hardened steel and rust = several broken drill bits and a real pain. Still doable, but takes some fun out of the job.