[Valiant]

Bot waypoints go into the following path structure:

.Nav files -> Fritzbot/bots/maps/
.Aiscript files -> Fritzbot/bots/scripts/
Both .cfg files -> Fritzbot/configs/
.script files -> Fritzbot/maps/
.arena files -> Fritzbot/scripts/

Files in Pk3 form can be placed directly into your ET/Fritzbot/ directory.
If you're savvy with Pk3's and Pakscape, etc - then you can pretty easily build this path and just copy/paste new waypoint files into a temporary pk3 to hold all new waypoints and fixes until the next version makes them official then simply delete the pk3 when the next FritzBot Patch (which generally will include them when possible) comes out.

This is more or less taken directly from the waypointing tutorial in the waypoint forum and my personal experience with my one or two little projects.