I could be off base but this is how I understand and utilize:
The working folder is the folder where your c3d projects reside. In my office we keep all our drawing project datat on the server which we use the virtual letter O:\, so I always say my working folder is the O:drive.
The data shortcut project folder is the folder where a specific civil3d project is: In my office that is the project root folder in the o:\
So when I create a new job I say the working folder is O: and the dS folder is the jobnumber folder in the o:, then I get created for me in each job folder a _shortcut folder with all the sub folders in it. Like this:
when I start a new drawing I go the the data shortcut node and pick set data shortcut project folder and browse the the job number folder in the o:\drive i need.
Could be a better way, but this works for me
Joseph D. Bouza, P.E. (one of 'THOSE' People) Civil 3D 2012 & 2013 HP Z210 Workstation Intel Xeon CPU E31240 @ 3.30 Hz 12 GB Ram
Note: Its all Resistentialism, so keep calm and carry on