Quick answers to your specific questions:
The lower the angle that you sharpen at, the "sharper" the edge, but also the weaker the edge. Putting a very-very small micro-bevel at a higher angle will give you a longer lasting edge, but it will perform better than if you simply sharpen at a lower angle to begin with. I wouldn't consider 15 degrees per side to require a micro-bevel. My micro-bevels might have a total included angle of 30 degrees. Caveat: I'm not a pro, so you might find that you need a 40 degree inclusive micro bevel on a 30 degree inclusive edge.
Putting a micro bevel on an edge doesn't make it more difficult with water stones, so I see no reason it would affect it with a sharpmaker. It only makes it more difficult if your micro bevel isn't micro.
With waterstones (and I'm assuming that it's the same with the sharpmaker) the stone that you start off with depends on how dull the edge is. If it just needs a touch-up, you will start with a finer stone. If you've gone through a number of touch-ups and it isn't holding very long, start with a coarser stone. You only use your finest stone to add a micro bevel at the end.
Don't count strokes on any knife. Examine your progress as you go. On a coarse stone, you raise a burr. On subsequent finer stones you reduce the burr (if you didn't strop it off between stones, otherwise you are forming a new, smaller burr) and remove the scratches from the previous stone. If you add a micro bevel, stop when the micro bevel barely visible.
I suggest that even if you want to use other methods, you learn about how sharpening on water stones. You can start here:
https://www.youtube.com/playlist?list=PLEBF55079F53216AB
Although the above videos cover a specific method for sharpening, what you are attempting to do to the knife at each step is essentially the same no matter what sharpening method you use.