armandxp:
What do you mean by "Main Directory"?
My iTunes music is right where I told it to go: in a "Music" folder in my iTunes Media folder.
As GGJ said, check your advanced preferences settings.
My advanced settings are the same as they were with my old computer, but when I bought my new air and installed iTunes 11, I made sure that I let iTunes manage my collection and keep the folders organized.
I just drag and dropped all my movies, tv shows, apps and books onto the iTunes symbol. I didn't copy ANY of my music, because it was all in iTunes match. But, when i did download a song, now from iCloud, it doesn't make a music folder, like it did create a 'apps' folder, 'movies' folder, 'books' folder. I didn't have to tell iTunes to make these folders, it just did it. Now, it doesn't make a music folder. No one will probably notice unless they start a new clean library.