Nah it goes in the root folder http://www.johnnysix.net/. Well the .htaccess file in the root folder will affect the whole site. You can put a .htaccess file in any folder eg. http://www.johnnysix.net/games/ and it will only affect that folder and sub-folders.
Hmm, I'll ask my host if I can do that, didn't know it was the server causing it.
I made a new version ( I guess Chrome only for now ) - increased the range of notes playable/quizable and added in the extra lines for notes outside the usual 5. I tightened up the graphics on level three also, as the extra notes required more space.