If you intend to use the two programs at the same time, select one program to auto-organize, and make the other just read the files from existing location.
1. Add new files using iTunes, and never auto-organize with MB.
2. Yes, but you don't have to delete any iTunes folder. Just make sure they are empty after your music files were moved. After transition to MB, never auto-organize with iTunes. If you rip CDs or create different format with iTunes, they will go to iTunes folder.
3. Add both track# and track count columns to the main panel. Or create a virtual field (Preferences> Tags(1)> Define new tags) like "track <track#> of <track count>" and add it to the main panel.