Doppler automatically imports files added to the Media Folder to your library. You can treat the Media Folder like any other folder — add your files and folders, name them however you want and then let Doppler import into your library for you.
Rename and reorganise files
When Doppler imports music, it also stores a reference to the file itself. This means that even after you've imported music you can rename and reorganise your files however you want.
Note: Doppler can only find moved and renamed files if they stay on the same drive. If you want to move your files to another drive (e.g. an external SSD or network drive), you should move the entire Media Folder using the "Change…" button in Doppler Preferences.