~iworx/bin/varpermsfix.pex --siteworx=domain.com will fix the files in the account/var directory (email, databases and stuff) but if you want to do the stuff in the html directory I think you just need to chown -R user.group * the contents of that dir.
DO NOT chown the entire contents of your user’s directory as that some of the files inside var are owned by other users!