jefferygarrett
Sounds like you have not read the manual as that is explained there.
http://wiki.contribs.org/Main_PageSee the Domains panel in server manager.
Create different ibays for each site/domain.
Note there is also good reason to put web sites into /opt (eg added security & protection from end users doing silly things, search the forums on this), although the practicality of that really depends on your individual requrements eg whether other people need to access and update the site files (which is easily done in ibays & not so easily done in /opt).