The best way to organize your files is to.... organize them. Some folks use folders that are in alpha (a-d, etc.) others use folder names (The Beatles, Miles Davis, etc.), some use genre. Mine are organized by band name folders and then within them are the individual albums (The Beatles>Sgt. Pepper, etc.). Individual albums by artists that have only one album or song are in individual folders with their name. Since you can look up music using folder view, (albeit only on either internal or microcard, not both at same time) you can search that way. Or once your tagging makes sense you can search by Artist or Album as well as by Folder. If you just dump song files into the Music folder willy nilly, good luck.
As to Commander One, it works very well. The biggest user error is to pull from your desktop, not from its desktop pane, into SP1000. It doesn't always like that. Just stay within the app and it's happy. Sometimes when you grab a file to pull over it grabs several and won't let go. Go up to the pull downs, choose Network or another choice, and then go back to Desktop mode. Now it works again. I moved my entire Music folder over using it with no issues (no way can AFT do that).
Duplicates? Good luck, that's for you to winnow out.