You're asking us to do alot of assuming here bit...
It sounds like you have an X-Y gantry system above a conveyor that brings blanks into the station. You have a ControlLogix processor (which one??) with a motion card (which one??) and a couple motors and drives (which ones??). On the business end of the gantry you have a machine tool of some type that will both drill holes and scribe lines, presumably with a common tool since you didn't mention tool change.
How am I doing so far??
Keith