Welcome to the Forum.
First, what brand of knives are you sharpening? The reason I ask is that different manufacturers profile the angle of their blades differently.
The Kershaw's I have usually come in around 19 to 21 degrees per side. This means using the 40 degree angle on the Sharpmaker (20 degrees per side). Follow the instructions and with a little time, the fine (white) ceramics on the flat side will get your blade shaving sharp. With time, you'll begin to feel when your edge is right as you pull it across the ceramic...there will be less resistance the closer you get to the right edge. Others here will include stropping, but I haven't found the need for that yet. I'm sure in time I will, in pursuit of the "perfect" edge.
I should predicate this on the type of steel in your blade. 440, AUS6 & 8 adapt very well to the Sharpmaker system. Harder steels take more time. I'll spend 20 to 30 minutes working a razor edge with the flat white ceramics on ZDP189.
Keep your stones clean. Use Comet or the like and a scrubbing pad like a 3M. Once the metal builds up on the ceramics, you'll get nowhere.
Flat stones are another issue completely. You have no guide for the degree of angle, and I would suggest practicing on cheap knives before you attempt this with a nice blade. There's a lot of information on sharpening with flat stones in the Tool Shed Forum.
I'm sure others will have a lot more to add...Good Luck!