in each b3.xml (hence each instance of the bot) you can specify where is the directory which contains the plugins :
<settings name="plugins">
<set name="external_dir">@b3/extplugins</set>
</settings>
also note that in the b3 config file, "@b3" is a shortcut to the directory where b3 is installed and "@conf" is a shortcut to the directory where the b3.xml config file is in.
If you are using the standalone win32 release v1.2.1 of B3, note that there is a but which prevents external plugins to load. Use the v1.2.2 beta instead