How to solve multiple itunes library issue..?

Okay, so today I got an alert saying that my startup disk is nearly full and that I should delete some files - this surprised me as I don't have 250GB worth of stuff, thus, clearly something was amiss. I ran OmniDiskSweeper and discovered that basically I have two copies of my entire (? - I'll get to that) iTunes library on my computer, so that duplicated 60GB is currently sitting in my hard drive pretending to be doing something useful.

When I go to Music->iTunes, there's a folder called iTunes libraries (picture 2), which contains an iTunes Media folder where all of my music *appears* to be, but there's also another iTunes Media folder (picture 1) just sitting in the iTunes folder, also appearing to have quite a lot of my music/films etc in. It seems to be running the one in iTunes Libraries, but I don't want to just bin the random extra Media folder in case there's stuff in there that's being used - is there any way of working this out? or is the best thing to do just to backup, breathe deeply, delete the extra folder, see what happens and restore if need be? On the other hand, OmniDiskSweeper says that the lone Media folder is 69.7GB while the Libraries folder (which contains many other files besides the Media folder) is 69.0GB.

I'd be very grateful for any advice, as I'm starting to think that a poltergeist is at work here. Thanks!