My itunes library is split between two folders, how do I condense down to one?

So I store all of my music on a seperate hard drive and I have about 211GB of music.  When I go into prefrences in itunes it says that my music is stored on J:/ My Music.  So when I click on that folder I can see all of my artists listed.  My problem is inside that folder of artists is a folder called iTunes and when I open it there is another list of artists with more music in there.  Now I have no problem listening or playing any of my music files in iTunes and I don't have a problem transfering tracks to and from our iPods.  Is there a way to get everything in one folder without causing a big problem?  The secondary itunes folder has about 75GB worth of music in it.  I have no clue how this happened or what caused it to happen.  Should I just let it go and not worry about it, or is going to be a long term problem for me in the future whenever I get a new computer?

- ITunes purchases by:
iTunes Store: Transferring purchases from your iOS device or iPod to a computer
- For other music you will need a third-party program like one of those discussed here:
Copy music

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