Alright, since you're gonna be doing a serious make-over on the way waypoints are used in FPSC, then here's where the waypoint stuff happens:
Search the source for:
_entity_controlwaypoints:
That's the beginning of the subroutine that handles a single entity's waypoint logic.
Now, where you want to stick the file reading stuff is entirely up to you, but I'd suggest reading either at the beginning of the executable, or near the waypoint structure; depending on if you want to have the file effect the executable as a whole, or if the file may be changing during execution (unlikely).
The path has been lit. Tread lightly.
The one and only,
Whosoever says, "Don't sweat the small stuff," is obviously not a programmer.