Concerning waypoints, I think you can only make them on a listenserver. And the editor has changed a lot. If you have used PODBot 2.5 before, you will notice loads of changes. The editor is much faster and easier to use now, but it takes a while to get used to the new way of controlling it. Console commands have disappeared 99%; all is now accessible via on-screen menus, and you can even bind each menu entry to any key you like.
If you would like to have some documentation (I currently have a pre-release version of it here) and some info on how to bind keys and get started, just PM me and tell me your mail addy so I can send the stuff to you.
And yes, you should really upgrade to a newer build of the dll. Right now the server is messed up and will be down for maintenance soon. But if you can't get R2b43 from the filebase...
http://filebase.bots-united.com/index.php?action=file&id=103
...(works for me), then you can also PM me, and I'll send it to you. With a newer AMX(X) version and an up-to-date bot dll, many of your problems ought to disappear.
And if it's not that urgent, you can just wait and get the next official release (r2b44 or 45) together with the finished documentation.

Should be ready after the server has been restarted...