I use sprut 7 here.
In the waterline op's there is a stock box that will leave stock for a second op, just put in what you want left in the stock box. I do this in the waterline roughing, then remove the stock value for waterline finishing.
in 2d contour there is a stock box as well. then use another 2d contour op with the stock set at 0.
You can also increase the diameter of the cutter when you set up the tool, it fools the software into thinking the cutter is larger than it actually is so the part is cut oversize.
Let me know what ops your using and I should be able to help. I have been using it for a bit over 5 years now, it was a bear to get a handle on initially though.........