Share 'Custom Jig Settings'

I set the piece that sides up and down, and the position of the step on the bit, differently than the width of the workpiece.  For those who hate reading and want to get straight to the question, it is, does it really matter if the bit goes all the way through the work piece, and drills a hole in the other side?  There are other details that I figure are relevant but if reading too much makes you…