It may not make a bit of difference one way or the other but I think I would like to have my domains separated from each other and not stuck onto the main one which set up the hosting account as an addon domain.
I stumbled across this on another forum and learned most of it comes from the limitations of cpanel. I don't know if this is true or not.
Does anyone have experience with the multi domain method over hosting several domains on one root directory? Is it even an issue. Do the search engines even care?
(edited to remove host brand name)