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When creating a new sub-theme, omega tools only offers multi-site locations listed in sites.php, but sites.php documents that you only need to list sites here you wish a "non-standard" mapping, like devexample.com => /sites/example.com
If your site is example.com Drupal will automatically find the sites directory /sites/example.com, so for the rest of Drupal, there is no need to add a listing for every site in the multi-site. omega_tools_sites needs to add in the directories under /sites into the list of sites, maybe with a check to see if they are writable by the user (this would be a plus, but not absolutely required).