Use the Folder and Filename check boxes on the Indexing & File Naming step in the Job Settings Wizard to indicate whether field values will be used to generate subfolders or filenames. Any field with the Folder option checked will create nested subfolders for each value in the order the fields are listed. Any field with the Filename checked will have the values concatenated to form the filename.
For example, if Field 1 and Field 3 have the Folder option checked, and Field 2 and Field 3 have the Filename option checked, image filenames will be created in the format:
%OUTPUTFOLDER%\Field 1\Field 3\Field 2 – Field 3.tif
The Filename Separator option on the Advanced tab lets you change the ” – ” between the fields in the filename to anything you want.