I can't answer for anyone but myself, and I'm sure some will disagree with my methods. All I can say is, it works for me.
1) Make sure the stone is setting flat on a solid surface. I prefer it to be at waist height, and I prefer to work standing straight up.
2) Grip the knife firmly just as if you were going to slice a thin shaving off the stone. I usually place the fingers of my off hand on the flat of the blade, with the thumb on the spine when stroking from left to right. This allows me to use my thumb for a height guide to help keep the angle constant. When stroking from right to left, my thumb goes on the flat of the blade with my fingertips on the spine so I can use them the same way.
3) Use smooth, LIGHT strokes. Trust me, those diamonds are way harder than any steel you are trying to remove, so let them do the work for you. I have ruined several DMT stones by using too much pressure in an effort to hurry the process. Too much pressure just rocks the diamonds until they cut their way out of the nickel used to bond them to the surface of the hone.
4) Once you decide on an angle, stick with it. After a few strokes on one side, you should be able to see where you are grinding if you look at the blade under a good light. I usually stick with one side of the blade until I reach the edge, which gives me a nice, flat bevel. Then I flip the blade over and do the other side until I reach the edge on that side.
5) Once I have the bevel established, I use successively finer hones to polish the bevel and get a finer, smoother edge. You can also go from a very coarse to a very fine and use a slightly higher angle to polish the edge only. That will look more like a Spyderco factory edge, but I prefer to polish the entire bevel. I feel that it reduces drag slightly so the blade cuts more smoothly. It also makes it much easier to see where you are grinding the next time you have to reprofile.
6) After you have done all that and used the knife, you can decide whether you need to use a lower angle to produce a sharper edge, or a higher angle to produce a more durable edge. If all you do with your knife is open envelopes and shave arm hairs, go low. I only go really low angle on a couple of dedicated whittling knives that never get used on anything harder than soft pine.
Hope this helps a little.