Music found in two separate locations and duplicate songs found

My apologies if this question has been asked before...
Recently one of my playlists "dissapeared." I searched a few forums and tried a few suggestions, but I felt the best resolution was to retrieve the iTunes library files from my backup. This worked fine, but I noticed one of the songs I recently imported was no longer in iTunes, but still could be found within the itunes folder in Finder. I figured this was not a big deal and something must have happened to the library database that caused it to crash. But this promted me to start looking at the folders and files in my iTunes library. First I noticed that I had the same music in two locations:
myHomeFolder>Music>iTunes>iTunes Music>Music and myHomeFolder>Music>iTunes>Music
But I found they were not exatly the same after checking the info of both music folders. I found the music in the iTunes Music>Music folder was about 4 times the size of the other. After viewing the files in the folders of the iTunes Music>Music folder I found there are duplicates of every song in every album in this folder. In some cases there are three copies of the same song.
Note that the same song is found within the same album folder. For instance: within the Billy Joel Glass Houses album I have the following files:
01 You May Be Right 1.mp3
01 You May Be Right 2.mp3
01 You May Be Right.mp3
My first question is why do I have two different locations for my music? Within iTunes I verified the only files in iTunes are in the iTunes Music>Music folder. So I assume I can delete the other folder. But this leads me to my second question - Why do I have two and three duplicates of the same song? And lastly what do I do about it? Should I leave everything as is? Shold I start deleting files? How do I prevent this from happening again?
I am using a MacBook Pro with OSX 10.8.4 and iTunes 11.0.5. I allow iTunes to consolidate my files and reorganize the files...
Thanks.

Two things to add to this:
First, one of music folder locations in my previous post is incorrect. It is not "iTunes Music>Music". It is supposed to be "iTunes Media>Music". I cannot figure out how to edit my post.
Second, I see pretty much all of the filenames of the music in iTunes has a 1 or 2 and the end of the filename. See the images. How did this happen, and how do i fix it?

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hello,
I tried searching the forums for a related questions but didn't find any. if it exists let me know.
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With my partner we are working on very havy image file from two different location. we wont to be able to share those file to each other easly and quickly mad make sur those file are allways up to date.
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Witch one of those solution seems the best and can work with MAC mini server? If you have another idea for my situation I m more then happy to read it.
Knowing that other user may need to access to my file, is the MAC Mini server VPN connection safe and fast?
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Chris.

The fact that you are both working on multi-gigabyte
files, the statement BDAqua made about network speed
is a big issue. Small incremental changes in a single
multi-gigabyte file still require that entire file to be transferred.
There in lies the big issue with network speeds.
Basically, it seems idea 1 will probably not work well and
besides, RAID is for local drives and not for over networks.
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Music found in two separate locations and duplicate songs found

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