TBH, I think you´ve done it right.
When we run a dedicated server for our collection of sites, our primary was public_html
so when you opened the server, you have all your other sites listed in alpha order and the members area, images and galleries, all the other content sub folders all listed amongst the first directory...
would have been better as public_html/primary
so now, these sub folders only could be seen when opening that site.
With the primary as the main folder, it was a cluster fuck, a mine field to first look at
