Best location for music?

The last couple of month I am re-organizing my music so it suits iTunes the best:

• 
  Converting FLAC to ALAC
  Filling blanc ID tags, especially album, as this is the default sorting
  Adding art (in the file itself)

Afterwards I have converted the filenames (with Renamer) in to "album, artist, title" so I don't need separated maps (which I don't like).

Now comes my question:
Is it better to put my music files in /Users/username/Music/iTunes/ or
or in /Users/username/Music/

And also another question pops up:
There are about 6000 music files and iTunes have a cache, but now most of my music files have art embedded in the file. Is it wise to clear my iTunes list, delete the entire iTunes folder (or one of it's subfolders), than copy the files to one of the locations in my first question and than add a new library in iTunes?

Thanks in advance!

Also I have noticed that sometimes in finder the file doesn't show a thumbnail of the art (like it is not embedded but only in the cache of iTunes). 99% are correct, but 1% seem to have a problem. Even copying and pasting the art again doesn't help, nor does adding the art via the add button...