When you import a CD in itunes it's different than when you import files. In first case it has to create the files and folders, in second case it's an option in preferences:
Preferences > Advanced Tab > Copy in itunes media folder the files added.
I suggest you uncheck this option so all files added to itunes are let where they are and aren't copied. But in case of CD itunes will anyway create the files and folders to import the CD and create the files.
Also in options, general tab, you have a button "import settings" or something similar (I don't use itunes in English). There you can change the formart of import, for example to mp3 at any setup you want instead of default probably some Apple mp4 setup.
If you move files and folders already in itunes or rename it you need take care that itunes find them because it stores a technical id. Also take care that : You copy the files somewhere like on another drive. Then move the original files and folder to trash. Then play the tracks in itunes and miracle it works. But then empty the trash and try again and itune will ask you the new position of the files.
If you want have organized music files I strongly suggest you to use another place then itunes music folder and use the change location ot relocate a file :
- Import the CD.
- Copy the files in the location you want.
- Go in itunes library and select the tracks imported from the CD, and delete and confirm they are moved to trash.
- Then drag the files/folder where you put the files copied into itunes.
If you have already imported the CD and added information instead you will want avoid delete the tracks in your library, so:
- Copy the files in the location you want.
- Go in itunes library and select the tracks imported from the CD, and select show in Finder.
- In Finder delete tracks and folder you want.
- Be sure you have copied all stuff you moved in trash.
- Then empty the trash.
- In itune select the first track then ittunes will ask you the location of the file, select your files copied.
- Repeat for each track moved.
EDIT: Those manipulations work only if you unchecked that option:
Preferences > Advanced Tab > Copy in itunes media folder the files added.