In Preferences-Save-iTunes Autoupdate I check:
Autoupdate iTunes library
Create iTunes playlist
Remove old reference
These three seem to coordinate well since 2.8.1. You can always have iTunes manually update tracks by selecting them in the Jaikoz-created playlist with the art window (lower left in iTunes) open. I do this just to be sure.
I leave Add new tracks unchecked. I prefer to add tracks via iTunes after I?m done editing in Jaikoz.
I think it?s also a good idea to leave ?Have iTunes organize files? unchecked in iTunes preferences during heavy Jaikoz edits. iTunes may move files around as you edit & save in Jaikoz otherwise.
I don?t use the Rename File or Rename Folder options in Jaikoz.