It's pretty simple if I'm understanding right. You use code to have the waypoints generate enemies, but to generate the waypoints, you have to use a sort of Create Object function and for the X and Y coordinates of it, use random values.
For example, if you had a room that was 1280x720, you could put something like this for the X and Y coordinates:
X: 200 + random(880)
Y: 200 + random(320)
This creates randomly placed waypoints, but with a 200 pixel border around each part of the room.