Marty,
I store all the raw (i.e. not yet reduced) data in folders that have a common naming convention like:
YYMMDD_TARGETNAME_SCOPETYPE
(for example: 150121_M42_SVQ100)
usually each of this folder has subfolders for Lights and Flats (which are specific to the night). I keep libraries for darks and bias, so those don't need to be in there.
Once I do the calibration and stacking, and I end up with master frames, I store those too in an appropriate subfolder.
To do the actual processing I use "projects" in PI. This is quite useful, as in the course of a project I usually end up creating dozens, sometimes over 100 files... I keep the project files in another drive altogether.
Hope this helps