This really depends, but I don't think it can be done the way you want it.
The 'supported' way
You can disable iTunes from copying music to the iTunes folder for future imports by going iTunes > Preferences > Advanced > Uncheck "Copy files to iTunes Music folder when adding to library". This will add all future files to the library, but it will not copy them into the iTunes folder, so make sure you do no.
The downside to this is that iTunes will not be able to keep those folders organized, so you would have to put them into the folder structure you want BEFORE importing them.
The hacky way
After importing the items into your library, move them to your alternate location, then create a symbolic link to the new location of the file. You have to use terminal for this:
ln -s /new/file/location/Britney\ Spears ~/Music/iTunes/Britney\ Spears
Assuming you moved the Britney Spears to /new/file/location/. The \ is used to escape the space in Britney Spears. This is important.
I have not tested this myself, so I do not actually know if it will work. I will try it out later and update this post
After further pondering, I have hypothesised a modification of the first method that should let you keep your ratings. After unchecking "Copy files to iTunes Music folder when adding to library", move the songs with the lower ratings to the external drive. Now, when you try to play the moved tracks iTunes should complain about the missing tracks. When it does, point it to the files that you moved on to the external drive.
If this works, it would be a tedious, song-by-song process which may be impracticable for a large amount of songs. You could also try going one step further by rechecking "Copy files to iTunes Music folder when adding to library" and hope that does not copy the files you just moved back into the iTunes Music folder.
Can you change where the downloads save to? You could chose the automatically add to itunes folder as the source for the downloads from Amazon.
I had just ticked the box to automatically add tracks to itunes, but this creates duplicates (files in amazon download folder and same files in itunes music directory). It does put the songs automatically in itunes, but the duplication is annoying.
Best Answer
iTunes does suck big time when it comes to keeping one's library organized (IMHO).
I uncheck the "Keep iTunes media folder organized" and also unceck "Copy files to iTunes Media folder when adding to library". That way, iTunes makes only one copy, and all files end up in one folder...
I keep my music organized via Media Monkey (http://www.mediamonkey.com/), and import it every now and then in iTunes (which makes one copy of the files, and I don't care if they are organized or not there...).
That's the best solution I found... I make Media Monkey keep my music organized in folders Genre/Artist/Song (songs move when/if I change their genre), and I edit the tags etc in Media Monkey. Then, I keep importing the same folder in iTunes - it's smart enough not to import twice the same song, even if it moves around. You do get an extra copy of your music in iTunes' folder, but I don't mind... I view it as a temp folder...