How are the PDFs being created? Are you dragging and dropping or is this through the solidworks add-in? The template tool can create subfolders based on variables from the input card. Not sure if that's what you are looking for?
In your PDF task under the output file details....the arrow to the right of how you can name the file....does it allow for the variables? I think they added this ability in 2017 instead of the 7-8 options they gave you before. We're on 16 here, but I swear I saw this option somewhere in a what's new get together or a document. If you can grab the variables now in 2017, just make sure that those variables are on your data card.
Yep it's in the what's new doc.