In that case, if Joomla is running in root, there should be no problem using JoomSEF to edit the .htaccess file in the root directory.
If you want to create some 301 redirects manually, just follow JoomSEF's documentation in Edit .htaccess file section:
www.artio.net/joomsef/documentation#htaccess
If you want to automatically redirect all URLs starting with /joomla/ to corresponding URLs without the /joomla/ part, you'll need to use the Advanced edit mode and create custom RewriteRules for that - this is out of scope of our free support, but we can configure it for you as a paid service.