Two media folders -- how to consolidate?

Hi,
I am using iTunes 10.5.1.42, Windows 7 Home Premium x64.
I noticed this morning that I have two iTunes media folders:
C:\Users\my_username\My Music\iTunes\iTunes Media
C:\Users\my_username\My Music\iTunes\iTunes Music
Both folders contain:
Automatically add to iTunes
Books
Mobile Applications
Music
The \...\iTunes Music folder also contains a folder called Podcasts which is empty.
Most of my music is in \...\iTunes Media, but some of it is in \...\iTunes Music.  Also, both Mobile Applications folders contain apps for my iPhone, but they don't have the same number of apps.
Preferences > Advances > iTunes Media folder location shows: C:\Users\my_username\Music\iTunes\iTunes Media.  "Keep iTunes Media folder organized" and "Copy files to iTunes Media folder..." are both checked.  Note that the top folder is My Music, but in iTunes Preferences it's just Music.  It seems that iTunes sees both -- My Music and Music as the same thing.  iTunes also looks in both iTunes Media and iTunes Music since all of my music is displayed in iTunes and on my iPhone.
I would like to consolidate the iTunes Media folder and the iTunes Music folder into one, but I want to be sure I do it correctly so iTunes continues to see everything and syncing with my iPhone continues to work correctly.  Note that I have not enabled iCloud and I only use one device, my iPhone.
I think I can simply copy everything from iTunes Music to iTunes Media (since Media is what's showing in Preferences).  Does that sound right?
Thanks for any help.
John

Hi Tom,
Do you have the iTunes Preference set as shown here? Keep iTunes Media folder organized?
Or have you tried File > Library > Organize Library from the iTunes menu?
For more info >http://support.apple.com/kb/HT1660?viewlocale=en_US&locale=en_US
Regards,
mm~

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