I've used TurboCNC successfully in the past to do exactly what you are describing on an X1. Basically, the gcode would move the table to the correct x y position then put a prompt on screen saying "Drill now" and would wait until the spacebar was pressed to continue to the next hole. I used the manual drill press feature of the X1 to drill the hole then pressed the spacebar to continue to the next hole.
It's been a while since I used TurboCNC but I believe the gcode was
Code:
( Move to X Y Position )
G00 X1.25 Y2.00
( Prompt )
M00 ( Drill Now )
( Move to X Y Position )
G00 X2.25 Y2.00
( Prompt )
M00 ( Drill Now )
The G00 will move to the correct XY position and the M00 will put the text of the comment in parenthesis up on the screen and pause the gcode program until the spacebar is pressed.