To answer your last question first, the book you want it "Penetration Tester's Open Source Toolkit, Vol 2.", ISBN-10: 1597492132. It covers a lot of the tools in B|T and has a chapter devoted specifically to B|T. That chapter was written by a Moderator on these forums, theprez98.
As to the rest, considering your experience, you're playing with fire, and the boss should be smacked upside the head. You should NEVER learn this stuff on a production network. If you do something bad, like say DoS the server, or accidentally delete work files, you and the boss could be in deep trouble with the non-profit's board.
Having said that, if you insist on going ahead, the protocol that you need to understand is called Small Messaging Block (SMB) which is used for "mapping drives" under MS Networking. The applications for doing this under Linux are known collectively as "Samba". www.samba.org
Good luck with this, although I would again STRONGLY urge you to confine further learning attempts to a lab, before you damage something and end up in trouble.