If you've converted the geometry to contours, BobCAD will assume you want it to cut in the direction that the contour is pointed. [Utilities] <Reverse Contour> can change that direction. If you haven't converted, then you can do something similar by selecting the parts of the geometry in your preferred order.
Man, I wish Sorin's videos were still up. He really explained all of that so well. Almost makes me want to "clean room" them, and cover the same topics in some Youtube videos...
Luke
"All I'm trying to find out is the fellow's name on first base" -- Lou Costello