The cgi-sys is kind of a system directory from which certain pages are provided to domains, like suspended pages, defaultwegpage etc..
It depends on what you want. Directadmin is build completely different than cPanel.
Suspended pages can be customized by /home/admin/domains/suspended same for reseller via the /home/reseller/domains/suspended directory.
For default pages to be provided when creating a new account use /home/admin/domains/default and samen for reseller (change admin to reseller). You can also put .htaccess there or custom error pages you want.