You can set up a macro to swap the axis. Say your drill is the B axis.
In the macro, put
SwapAxis(2,4)
and call it before driling and Z commands will now move the drill.
After drilling, call another macro with
ResetAxisSwap()
I'd recommend using one offset for routing and another for drilling. So if you use G54 when routing, you need to call G55 when you do the SwapAxis. The G55 would contain the offset info from the router to the drill. And when switching back, call G54.
One issue you might have is if you use the Zero axis buttons, you'll be changing the G54 or G55 values, which you don't want to do.
You're going to have to learn to write simple macros to do this.