The best place for sv_pure is in your personal autoexec.cfg, tho it can go in your server.cfg also.
If you're planning on using your custom bot files on a dedicated server, it'd be better to encapsulate them in a pk3 file. Then your clients will automatically get it downloaded and installed when they connect the first time. That's easier that trying to get them all to go unpure and also shuffle files and folders around. Crapshoot has created a pk3 template that you can use to make one of your own. You can get it at
http://members.cox.net/knickel/fritzXX.pk3.zip . Read the Readme file included in the zip for instructions.
Vvlttch has more experience in running a server than I have. Perhaps he can step in and describe how to set up your bot files to run a campaign, for instance.