iTunes on a Mac may be more forgiving if you move things around manually, but it isn't really recommended.
Here are typical layouts for the iTunes folders:
If you have upgraded from version 8 (or earlier) to iTunes 9 (or later) at some point, then your media folder (everything inside the red outline) may still be called iTunes Music instead of iTunes Media. The extra Music folder inside the media folder is used if you had an older library and have allowed iTunes to Upgrade to iTunes Media Organization (iTunes 9) or used File > Library > Organize Library > Reorganize files in the folder "<Media Folder>" (iTunes 10/11). Depending on your choices for Keep iTunes Media folder organized and Copy files to iTunes Media folder when adding to library plus a little bug in which one build changed the name of the file storing the choice of layout it is quite easy for some of your files to be organized according to one layout and some the other. (Recent installs of iTunes on a Mac now give the library file the .itl extension)
Assuming you're happy letting iTunes organize your files the following steps should tidy things up (should it be necessary):
1. Select File > Library > Organize Library... > Tick Reorganize files in the folder "<Media Folder>" and click OK. Skip if this option is grayed out (already upgraded) or you prefer the older layout.
2. Select File > Library > Organize Library... > Tick Consolidate files and click OK. This will bring any files currently organized outside the designated media folder into it. N.B. This will create duplicate copies of any file that needs to be consolidated, and you will need to manually clean up afterwards.
3. Select iTunes > Preferences > Advanced tab, uncheck Keep iTunes Media folder organized and click OK.
4. Select iTunes > Preferences > Advanced tab, check Keep iTunes Media folder organized and click OK. This triggers iTunes into reorganizing everything according to your preferences.
5. (Optional, if applicable) Close iTunes, rename the media folder iTunes Music as iTunes Media then restart iTunes. Check under iTunes > Preferences > Advanced tab that the location has automatically updated. If you can't access the media for any reason just undo the folder rename.
PS If you really prefer the older layout, but it is already in the new one then, edit the hidden file .iTunes Preferences.plist in your media folder and change the integer from 1 to 0 before doing step 3.
You should backup your library before attempting any major reorganization.
If iTunes is still creating files or folders in the wrong locations there is a possibility of permissions problems. Offhand I'm not sure of the correct OS X terms but on Windows both the system and user accounts should have full access permissions to all files & folders within the iTunes folder in order for it to work properly.
tt2