A couple tips I have learned are; first, trim all your cases to the exact same length before deburring the flash-hole. Second to get the right depth of cut I loosen the collet on the first case and then cut untill I feel that the burrs are off and am just starting to cut through a full turn, don't press too hard!
Then set your collet with that case and do the rest. At least that's how I do it.
I used to do it like Devildoc, until I got the sinclair tool, that has a sliding sleeve over the cutter, so you can index off the inside of the head and cut a nice small radius regardless of the overall length of the brass (much easier/faster).