MacBook Pro :: Consolidating Copy Of ITunes Folder On External Drive Via Terminal

I've recently got a new MacBook Pro, and for at least 6 years or more, I've been using Windows to handle my iTunes library. At one point, when trying to transfer my library, somehow I lost ALL my music. As a result, I learned to back it all up...And I learned to be patient when doing so. Any way, I want to make sure that when I transfer my files THIS time, I do it right. I just need to consolidate my iTunes library that I have backed up to an external hard drive to another folder on the same drive.

Then when I move it to iTunes on my Mac, I only have to put the files into the "Automatically Add to iTunes" folder. That said, I'm fairly decent with using the terminal; I've used Ubuntu for a while, and right now I'm using Fedora. I would use the terminal on my Mac, but I really don't want to use it there; I'll stay safe and let my Fedora computer do the work. That said, I know that both Mac and Fedora have "rsync" and "find" as part of the UNIX kernel both are built off of. With all that out of the way.

My question is simply which commands I ought to use to manually consolidate the files in the iTunes folder to a separate folder on the same external hard drive. I also happen to have a number of duplicate files, for some reason, except the duplicates are sometimes .mp3 files, while others are .m4a files. While the majority of my music has been restored because of "Purchased" section of the iTunes Store, I'm unsure of which files I'm looking to preserve; Do I just copy the mp3 files, or both? I hate doing music database repair.

Info:
MacBook Pro, Mac OS X (10.6.8)