How do I create a new iTunes folder?

After moving backwards and forwards between Mac and PC, different format hard drvies and versions of iTunes (I recently "downgraded" back to iTunes 10.7) my music folder is in complete chaos. There are duplicate files, folders all over the place and deleting music from iTunes doesn't remove their folders. I'm wanting to have a huge clear out and basically rebuild my library and the folder itself from scratch, but I'm having trouble doing so.
Currently my iTunes folder is on a FAT32 partition on an external hard drive and what I would like to do is create a new, "empty" iTunes folder on the NTFS partition, then pick and choose which mp3s to copy across, leaving behind all the stuff I don't want to be deleted once I'm done. I tried doing this by making a new library, but all the actual mp3s are still being kept in the same place. Basically I want iTunes to ignore the folder that already exists long enough for me to copy the stuff I want to a new one. The best way I can describe it is that if you were to install iTunes on a new PC, it would create a folder without any actual music in it, then you could drag and drop mp3s from your old folder into iTunes itself, filling the folder up.
I hope this makes sense to somebody who can help me out, thanks!

assuming iTunes is authorized for your iTunes store account(s):
connect your iDevices (one after the other) and right-click or control-click them in the iTunes Source list, then choose transfer purchases from the shortcut menu that appears.
above will cover your purchases. for everything else, check out this post by Zevoneer.
also, there are PhoneView and iRip.
when done, go iTunes > preferences > advanced and point iTunes media folder location to the new external. on the same tab, ensure the copy files ... when adding option is checkmarked.
next, go file > library > organize library > consolidate files.
Back up your iTunes library by copying to an external hard drive

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