Hi Charlie,
Here are some pics. the first is the best example I have on hand, it's that lip on the bottom. I got my planned correction straight in my head and tried it, here are the results

I added .0625 to the project canvas, kept the Z of the model right at the top, also added .0625 to my leave stock setting on the roughing pass. When I did the finishing pass(1/8th ball nose) it cut down that extra .0625 into the spoil board leaving a nice clean edge, very little sanding needed. It was a little more murderous on the spoil board than I had hoped, but I guess that is what it is there for. So does that make more sense and is that the right way to do it?