I'm not really sure what you mean by that. I'm really not sure what tool to use when. I keep experimenting with different tools but just don't know how to manipulate the work plane to where I need it.
I included a new drawing in which I left the holes long, as Henry suggested, and was able to 3d subtract them, I think, from the outside of the drawing, but I can't get the work plane to the insides so I can trim off the excess length there. I'm under the assumption that I have to get the work plane (red square) to the inside surface so the program knows where to trim the holes to. Is that correct or not?
I highlighted in red the holes that need trimming. I managed to get the holes trimmed flush with the outside, but not the inside.