Problem: I am applying toolpath to a surface but it is machining the wrong side of the surface.

Solution: Unlike solid models, surfaces have a positive and a negative side. You can see this in GibbsCAM by clicking on the Indicate Sheet Side button

One side will display as red while the other is blue. If the side you need to machine is red select the surface (it will turn yell) and go to Modify→Toggle Sheet Side. If you de-select the surface you should see that the red and blue sides have swapped.