use these binds below and it should work for You with podbot mm V3 version.
Note:
You can make waypoints only on listenserver - You create a game and play on the same PC.
//U = Main Menu
bind "u" "pb wpmenu"
//I = Turn on/off Auto waypointing
bind "i" "pb wpmenu;menuselect 9;menuselect 2"
//P = Pathwaypoint Add
bind "p" "pb wpmenu;menuselect 5"
//o = Pathwaypoint Delete, and answering YES to "Are you sure?"
bind "o" "pb wpmenu;menuselect 6;menuselect 1"
//[ = Waypoint Add Menu
bind "[" "pb wpmenu;menuselect 1"
//] = Waypoint Delete, and answering YES to "Are you sure?"
bind "]" "pb wpmenu;menuselect 2;menuselect 1"
//; = Flagmenu
bind ";" "wpmenu;menuselect 4"
//F6 = Waypoint Setradius Menu
bind "F6" "pb wpmenu;menuselect 3"
//F7 = Cache waypoint
bind "F7" "pb wpmenu;menuselect 9;menuselect 7"
//F8 = Waypoint check
bind "F8" "pb wpmenu;menuselect 7"
//F9 = Waypoint save
bind "F9" "pb wpmenu;menuselect 8"
All these lines above starting from 'bind' You should place in Your config.cfg file placed in Your ...\cstrike (or ...\czero) folder (it depands on the mod You are playing).
Once You get it working read carefully both section about waypointing in pb mm docs.
The first one lets You understand what every kind of waypoint is supposed to do,
the second one will prevent You to make some stupid mistakes as unnecessary connections, unnecessary waypoints etc. Ask
Ancient for more details - I've been talking to him last days to let him understand the waypointing stuff. I just don't have time to teach everyone separately.