ITunes organizing music into two totally separate places

I've been using iTunes for as long as I can remember, and ever since I picked up an external hard drive, I've been backing up my music constantly. I noticed a year ago or so that my music had been split into two separate places for no apparent reason.
My music is currently in these two places:
iTunes Media >> Music
and
iTunes Media
Why? I have no clue. I don't know how it got that way, and I don't know why a program would ever organize music in such a way.
The worst part: My CDs are split across these two folders. For example, the album "Strawberry Jam" by Animal Collective is split across these two places (tracks 1-4 are in iTunes Media, tracks 5-9 are in iTunes Media >> Music).
I don't know about anyone else, but I find this incredibly frustrating as I want all my music from one artist in ONE FOLDER, not split across two directories.
Any idea on how I can fix this and keep iTunes from splitting my music up in the future? I'm rather ticked off right now as I just deleted a bunch of things only to find out that half of the CD is still floating around in the other folder. I really don't want to go through my entire 140+gb library, move each album individually, and then re-load it all into iTunes.

I'm not certain I've understood what you would like to do. From my own experience, I find that it's easier to work with playlists. Before importing a new CD, I create a new playlist into which I import the CD tracts. Then I edit the track information: name, sort name, composer, album, album artist, etc to insure uniformity and correct track sequence and organization. Within a playlist, I select the first track, then go to "get info", and click on the "sorting" tab. In that tab there are 2 columns one for the display information and one for sorting information. Because I use an iPhone and an iPad where display space is limited, I label the tracts as follows:
Beethoven: Symphony #1 C 1-Adagio Molto, Allegro Con Brio
Beethoven: Symphony #1 C 2-Andante Cantabile Con Moto
Beethoven: Symphony #1 C 3-Menuetto: Allegro Molto E Vivace
Beethoven: Symphony #1 C 4-Finale: Adagio, Allegro Molto E Vivace
For the "sort name" I use simply "Beethoven: Symphony #1-1" etc.
I have all of Beethoven symphonies in one playlist, each set by a different orchestra & conductor in a different playlist.

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