If you are using SheetCAM TNG there is a POST included called MP1000-scriber that Les from SheetCAM wrote. It allows you to define an offset (in X,Y and Z) and just call a tool number GREATER than 100 in SheetCAM so you can go around and mark hole center using a "drill" tool or other things using an engraver type tool. You don't have to burn two different Gcode files and you can even intermix the two processes if you want.
If you are not using TNG then contact me. I have a Dual Axis Z POST that is being used on a custom table (has a plasma torch and a spindle) that does multiple operations and drills/routes, then cuts larger sections with plasma. I used a different method than Les did with the MP1000-Scriber. I just applied a G52 offset call (and cancel at any toolchange) and used the tool number to swap axis calls (we used B for the spindle axis) It has separate motors on Z and B but it should work with some modification to use just Z but with two different tool holders.