Okay I'll reply just this once, but yeah, remember PM's are quicker and less cluttering if you're just asking one person something.
; )
Bot routes are stored in "wnt" files which are stored in a pk3 file in my /base folder.
For examples, check out DDS Re-Routed (downloadable from LucasFiles.com) and look at the directory structure in the Pk3 (open with winzip). The files have to be in the proper directory structure to work.
http://www.lucasfiles.com/?s=&action=file&id=375)
To create the wnt files is a bit more complicated, but much much easier than editing most other things in JA:
http://www.perkwerx.com/DDS/TUTORIALS.htm)
Follow this tutorial and you should be on your way!
Tips: using 1.01 you may have to "load the map with cheats" several times before it works properly. You can always check the console (scroll up with pageup/pagedown to see if it loaded the routes correctly when you're done). Also realize that a BIG route may take awhile to save (I've had to wait up to 5 minutes before for a really long one). It's even longer if you had errors which it tries to automatically correctly. Generally you have to make the route in one shot, so do the best you can, plan it out on paper in advance if that helps.
Also I've been told that you may have to have your graphics settings turned up to view the floating numbers properly (not your resolution, but the other settings shouldn't be turned off).
Finally, the shortcuts he provides may or may not be useful to you. In my case I just edited my own files and did it that way, since I don't have JA installed in the default directory, etc.