Okay, so I think I've figured it out a little further.
qb.conf.wintemp is the template for the supervisor on windows and temp means template not temporary.
qb.conf.win32 is the worker qb.conf, these go in the Windows directory on the worker's machines and this one is related to the qbwrk.conf for doing automating the distribution.
qb.conf.client and qb,conf.supervisor the Linux equivalents.
Is that all correct? What is qb.conf.template's job?