There are several ways to make holes, I'm not quite sure how you are trying to do it. If you have a block and want to put a hole it it, you can boolean it if it is for faces or Stencil the hole then do a bevel on it. If sub'D, you can select the poly and do a smooth shift, adjust the points and then do a bevel in. Depending on how close up you are going to have the camera, you don't really have to show any threads going down if they are covered by the tuners.
If just holes, then you can always create the threads, flip them inside out and bridge them to the block, but that would usually mean that you would need quite a few poly's on the block to be able to bridge it cleanly
