Sync itunes media folder with library
For every song the you import into iTunes, a copy will be made in your iTunes Media folder. If you want to delete a song from iTunes, I would suggest you do it by right clicking on the song and hit delete. Then it will let you decide if you want to remove the referente to that song in iTunes or move the file (the one in iTunes Media, not your music folder) to trash.

If you need to open a different library or reload one, make sure iTunes is closed and click on the icon while holding the option button on your keyboard and then navigate to your iTunes Media folder