ok,
1. go into ur repack\scripts\extra folder and make a folder called "ways" without the quotation marks (This is case sensitive so type it exactly how i say it)
2. log onto ur private server
3. make 2 macros
4. have one have .startway and have the other one .addwp
5. go to the position you want ur waypoint to start and click on the startway macro
6. go around and keep doing the addwp macro (the character will go in a straight line to the next wp)
7. when ur done then go into ur repack\scripts\extra\ways folder and click on the file that says Ways******* and look at the first waypoint, copy the waypoint number then at the last waypoint type in next=#####(the number you copied)
8. go back into ur private server
9. do .mergewp, i think thats right, if not then do .mergeway
10. do .rescp
11. now pick a spawnpoint and do .setwp #####(the number you copied)
Congradulations! you have just made a waypoint!
Notice: You will say .startway and .addwp in chat, but dont worry! it still works!