Lets say I have two sub tools, a sphere and a cylinder. I want to subtract the cylinder from the sphere. First I make sure that the subtracting tool (in this case the cylinder) has less polygon count than the main tool to be subtracted from (in this case the sphere). I choose the subtract icon in the subtracting tool (cylinder)
Selecting the tool to be subtracted from (sphere) I go into dynamesh mode (Tool>Geometry>Dynamesh>Dynamesh Button)
After this I choose to merge down (Tool>Subtool>merge>merge down button)
Once the tools are megerd I redynamesh (Ctrl + Drag on the graphic area).
Done.