How do I reorganize folders outside of iTunes to get them into my iTunes Media folder - and without duplicating them?

Currently use iTunes 12 on a PC. I have music, that is in my iTunes library that are in folders outside of the iTunes folder (i.e. Amazon MP3 and iTunes Music). I want all of my music to actually reside in my iTunes/iTunes Media folder - and have the library point to the songs in that location. If I use the "Organize" function it won't pick up music outside of the main iTunes folder. Any ideas - and I don't want to "duplicate" the songs and have to go back and delete them - the library is over 13,000 songs with about 10k in the iTunes Music folder. Right now when I add new music it will go to the iTunes/iTunes Music folder and that's were I want all of my music to be. I'm moving from a PC to a MAC and want to only have my music in one place - so am trying to clean up before I use Migration Assistant so that it all comes over ok - don't want the dreaded "!" when the links get broken. Thanks.