For some reason files a still saved in the 'files' folder in the root of my drupal installation and not in the 'files' folder in the domain folder under sites. Any ideaes why that is?
That setting is in admin >> settings >> file system - you can specify the folder there.
Secondly.... I can't seem to enable clean urls on my sites, but it works on my base installation. Some settings I need to change in vhost?
Joe
Maybe check your settings.php first for base url etc.