Making waypoints is hard at first, but once you understand how things work, everything will appear to be easy.
What you should first do is download waypoints that have already been made and look at how they work on different maps.
However, making a map for the game has proved to me, to be very difficult and very time consuming.
Generally, a good waypointer will place waypoints in a map and have everything done in 15 - 45 minutes. It is also time consuming but not as long as making a map. lol
The waypoint menus for YaPB, e[POD]Bot and Podbot MM will only work on Listenservers, so you will not be able to make waypoints on a dedicated server.
If you choose to attempt making waypoints, let me know I'll point out some errors and how it is supposed to look.
It's the best way to learn how to waypoint, especially since I taught 3 other people the same way and they made pretty good waypoints.
I also have a special key bindings for waypointers, it doesn't use any game play keys, unlike SoulFather's bindings.