This *is* annoying in cPanel. But there are two other options (only second one is possible on HelioHost) to have all domains files (including main one) in separate folders. First option to deal with it in cPanel is to have all addon domains pointed to the folders outside of the main public_html. This is *intentionally* not possible on HelioHost. Second option is to use .htaccess rewrite engine. Create new "maindomainfolder" folder inside of public_html, move all main domain files in there and directly in public_html create .htaccess with something like:
RewriteEngine On
RewriteBase /
RewriteCond %{HTTP_HOST} ^(www\.)?maindomain\.com$
RewriteRule ^(.*)$ /maindomainfolder/$1 [L]There may be conflict with other rewrite rules in other .htaccess files inside that folder, some modifications of them may be needed to reflect folder changes.