I recently started converting an existing PHP project to CakePHP and YUI 2.8. The first decision that I had to make was where to place the YUI CSS files. I tried to find a quick, yet elegant solution, but I ended up with solution that was not so quick (or elegant).
I copied all of my YUI files from webroot/js/yui/ to webroot/css/yui/. I then opened each folder under webroot/css/yui/ and removed all of the js files (leaving the assets folder). If a folder contained js files only, then I deleted the folder.
I opened each folder under webroot/js/yui/ and removed all asset folders and css files. If a folder contained css files only, then I deleted the folder.
I spent about an hour trying to find another solution, so I guess the few minutes it took to remove the files/folders was worth it.