I assume you are worried about pin holes coming out the opposite side on the same plane they went in at.
First, for most drilling I like to have the stock with the barrel in it in a vise. I use the barrel as a plane to set a small level on.
I'm convinced that it is often the part that you are drilling for that deflects the bit so I do it this way.
Mark both sides of the stock where you want the pin. Center punch with sharp pencil.
Drill from one side as straight and level as you can until you hit the metal part your pinning...give it just enough more to dimple the part.
Flip it around and drill as straight as you can from the other side until you hit the part again....you could drill through it at this point or take the part out to drill it through.
Just like anything else in gun building, techniques, opinions and results will vary by builder. :wink:
Hope this helps, J.D.