Installation walkthrought for dummies ;-) : 
http://forums.bots-united.com/showthread.php?p=24879#post24879
It is intended to have 2 different joebot folders, that's no fault. one containing the dll / so, the readme and information about creating waypointing in the hl folder. in your mod's folder there is another joebot folder, containing the bot.cfg, joebot.cfg, bot_names.txt, bot_skill.txt, botbuyweapons.cfg, nn.br3, nnc.br3 and the spray.txt. there you can also find a folder for the chat files ( /chat/ ), another folder for personalities ( /per/ ) and last but not least the folder for waypoints ( /wpjs/ ). This folder contains folders with waypoint files in it ( *.wpj ) and a file called dir.txt defining the priority after which the folders will be searched for usable waypoints.
JoeBOT has currently 2 different libraries, one for MetaMod and one 'hook'-dll. Both version work, although we recommend to use JoeBOT on cs1.6 using MetaMod, which provides additional functionality.
A french tutorial made by Devil can be found here : http://csbots.cs-expert.com/index.php?fonction=dossier&id=28
Steam CS: c:\program files\steam\steamapps\your@email.com\counter-strike\
Steam Dedicated Server: c:\program files\steam\steamapps\your@email.com\dedicated server\
see http://joebot.bots-united.org/readme.html for command details
/Note from ok:
for me the linux 1.6.5.1 download from SF did have the joebot .so files in the same dir as the resource files (wpj/txt/..), and it worked with adding
linux joebot/joebot_mm_i386.so
to my metamod's plugins.ini.