you can use the variable NUKE_PATH on every machine to tell Nuke about custom plugin directories.
In that custom location you can use files called init.py and menu.py to add more source directories and customize settings, interface etc.
I personally recommend using the NUKE_PATH to point to the base location(s) and using the init.py in there to source any sub directories to keep your files in order (rather than dumping them all into one location).
The init.py will be read first everytime Nuke starts while the menu.py will only be sourced for an interactive session (i.e. not for command line renders).
Check out the chapter "configuring nuke" in the manual for some more details.