Quote Originally Posted by bdominick View Post
Okay, the addons option works for now. Eventually I'll want to switch the primary domain to use the same doc root, but for now this works in a way I did not expect. Thanks Matt!
If that's the case why not move:
/home/[username]/public_html/subfolder

To:
/home/[username]/subfolder

Then delete public_html, and rename subfolder to public_html

That's the cleanest way to do it to make sure that it will be easily compatible with cPanel and not getting into httpd.conf

That takes care of the main domain using the correct document root. The addon domain will break since its document root no longer exists but that is easy enough to fix by simply adding:

/home/[username]/public_html/subfolder

or removing the addon and parking it instead, on the main domain since that sounds like what you are trying to do anyways.