Jim, how was it the second time through?
Robert, I guess that intersect thing is sort of Boolean. Take your rod through the plate example. If you place the rod through the plate and then run Intersect, SketchUp will then create edges between the faces of the plate and the faces that make up the sides of the rod. If you delete the rod on either side of the plate and delete the faces inisde the perimeters created during the Intersect operation, you're left with a hole.
Clearly it would be easier to draw a circle on the surface and use Push/Pull if you just want to drill a hole but suppose you are drilling a hole at an angle. Even suppose you are drawing the hole for a pocket screw and you want to drill the hiole exactly as the special pocket hole drill bit would make it. Draw the stepped drill bit, set it at the proper angle and then move it into place in the "wood". Intersect with model and delete the drill bit that is exposed. Delete the ellipse on the face of the board and you have your hole for the pocket screw.
Another way to think about what I did with that bracket is this. Imagine I had a shaper cutter ground to the shape of that arc. I just ran the cutter across the wood and presto!
For another example of this, go back to the Design. Click. Build. blog and look at the video I did showing how to cope the end of a rail for a frame and panel door. I used the exact same technique for that.