It's not difficult at all, Steel. I use the Sharpie test if I'm particularly concerned, but most of the time I just put the knife about halfway up the blade in the clamp and it works just fine. To use the sharpie test with the WEPS, just black the edge, put the fine paddles on, and make a light stroke up each side. Make sure that the marker came off about the same way along the entire bevel. If it's still black on the edge at the heel and not in the belly, move the knife forward. If it's on the edge at the heel and not at the bell or tip, move it back.
There is a log book included with the set for you to put down your settings for individual knives, there's a scale for front-to-back placement, and the angle guides will tell you the per-side angle. Just log those down, and you can go right back to the settings you were using the next time you put that knife into the clamp. I would suggest picking up the 800/1K diamond plates as well, they make a big difference. Although you can easily go as high as you want by just taping wet-or-dry sandpaper to the 600 paddles and continuing to work your way up. I saw a Hinderer a while back that someone did that way and showed off a lot of pictures.
I really like my WEPS, it's efficient and easy to use. You'll undoubtedly hear a fair bit in short order from the "freehanding only!1!!" crowd, but I really like mine.