Watch the dvd included with the sharpmaker, then watch it again. Sal from Spyderco explains very clearly in a soothing voice exactly how to use it. Stop worrying so much, the sharpmaker is an incredibly easy sharpening system to use. You're WAY over thinking this. The bevel is simply what you probably call the edge. Setting a 30°inclusive bevel with a 40° microbevel just means that the visible "edge" that you have on your knife is at 30° and you have then sharpened or touched up your edge very lightly at 40°. It really isn't that complicated. Your pm2 probably has a factory edge (bevel) angle of around 30°. It doesn't matter if it's 28° or 32°, just sharpen at 40° to start with. After you have sharpened your knife a few times at 40° you will notice it will start to take longer and longer to sharpen each time. This is because you are effectively widening your 40° bevel requiring you to remove more metal each time. When you start to notice the 40° setting beginning to be less effective simply make 50 or so passes on each side on the 30° setting with each set of rods. This will knock the "shoulders " down a bit which will allow you to more easily reach the edge on the 40° setting. All of this will be explained in better words than my own in the dvd.
You clearly didn't watch the DVD. Using the 40 degree setting on a 30 degree edge will remove a ton of metal. The 40 degree setting is made to back bevel so that you can then move to the 30 degree setting.