Bob,
Knowing your machine controller and CAM system would help.
Mach3 has an included Nesting Wizard which allows you to create an array of parts in a grid with X and Y offsets of your choice with the G Code for just one.
Many CAM systems have nesting options.
It's often possible to set your part zero or a known coordinate in an area of your stock which doesn't need to be removed until the second side is machined, place a through hole at this point and you have a reference for setting zero on your second side.
What you do in CAM for your second side will be dictated by your chosen work flow.