I set up the SharpMaker with the corner in on the left stone and the flat in on the right. I do alternating heel to tip and tip to heel strokes on the left to ensure I'm hitting both sides of the scallops, and I tip the blade to put the flat of the blade flat on the stone when I do the back, but scratches don't bother me. On the rare occasions (like maybe once a year) that I need to sharpen my K390 SE Police4, I run through diamond, then CBN, then brown and white ceramics and sometimes even break out the ultra fine rods.
Serrations are ground all at once on a shaped wheel. All the scallops are parallel. You need to pay attention to all three axes when sharpening serrations. Roll and yaw obviously affect the edge angle, but for serrations, the pitch is critical. Find the blade pitch that aligns the centerline of the scallops vertically and keep it there. If you get the point too high or too low, the rod corner won't ride in and out of the scallops, it will bridge across them, grinding away the points and leaving the rest of the scallop untouched. Some rounding of the points will occur and actually helps make the teeth less prone to snagging, but too much and you don't have serrations any more.