Which ones need their docroot moved?
We can move them for you, but keep in mind that if your scripts care about the name of a docroot, they're poorly written. Good scripts won't care where they are located.
You should be using relative paths to reference files within a website, and if multiple sites are doing something like sharing includes, you'd be best served by moving the shared files outside of the docroot of another website (e.g. instead of a script for one domain needing a shared include referenced as ../../otherdomain.heliohost.us/public_html/includes/something.php, move the folder containing the shared components into your home folder and edit the sites using them to reference it as ../../includes/something.php).