"keep folders organized" feature duplicated my itunes library

I recently downloaded and installed the latest version of itunes for windows vista. During the installation, I was asked if i wanted itunes to keep my folders organized, or if I wanted to do it myself. I chose to have itunes keep my folders organized. I then closed itunes. The next time I opened itunes my library was duplicated, thus causing my library to double and preventing my ipod to load new songs, saying there is not enough space due to the duplicate songs. I looked at each of the duplicated song's info and noticed that one of the files is located in the folder "itunes library", while its duplicate is located in the folder "itunes music". I then went to both of those folders and noticed the "itunes music" folder holds a folder for each individual artist and their respective albums, while the "itunes library" folder just has every individual song file, listed alphabetically. Should I just delete one of these folders, and then remove the dead files from my library, thus removing the duplicate entries? And if so, which folder do I delete?

If you want iTunes to keep it organized in artis/album format, then delete the other folder that has +every individual song file, listed alphabetically+.
I'd try it on just one song first, to make sure you have it straight.

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