In my 3d drawing program, not sketch up we can make a "cutting block" and put it where we want the cuts to be made and make it the male part and tell the program to remove the female part.
We use these cutting blocks all around where we need them and them delete them afterwards, but save the original in our library.
As I don't draw with sketch up I'm not sure if this process of male and female cutting is even available.

Good luck with your research.
Jim Rogers