You could set the upload folder to just "img/" in the config.php file and then specify a different sub-folder for each instance.
If you find this line on your page:
$CKEditor_config["filebrowserBrowseUrl"] = "../webassist/kcfinder/index.php?
then you can add a url parameter: &startup_folder=subfolder&showsidebar=true
and if you set showsidebar to false then it wouldn't allow them to change the folder from within the interface.
For either of these to work you will need to make sure you have the latest version of the extension, since there were a few issues with previous builds.