TDT can automatically synchronise files between your PC and player. Since it uses tag information rather than filenames to decide what is on what HD, the folder structure on your PC can be completely different from the player's layout. This process is completely automatic, simply check the Synchronise|Enabled menu item and scan the player.
Files on the player are created with the pattern specified in the Edit|Rename Files From Tags dialog. The pattern used to form any new filenames on the local PC has the same syntax as the tag-renaming dialog and is changed via the Synchronise|Local Folder Structure menu item. Use the Synchronise|Select Local Folder menu item to select the "root" folder containing the music on your PC.
Files that exist on your player but not on your main PC can either be ignored, copied to the PC or deleted from the player. Files on your PC but not on your player can be ignored or copied to the player. Files which exist on both player and PC but differ in their tag information can be copied depending on the date/time they were last modified – newest copied over oldest. Use the Synchronise|Ignore Rating Tag menu item to make TDT consider files which differ only in that tag to be identical.
If the Synchronise|Quick Sync menu item is unchecked, TDT will present you with the lists of files to copy – use the Delete key to remove any selected files from these lists (and thus prevent them being copied.) Use Synchronise|Copy To PC and Synchronise|Copy To Player to control where files are copied to.