I apologize if this is in the wrong forum section as I could not find a cPanel section

What is the purpose of the main domain? I have a hosting plan with HostGator that allows unlimited domains, and therefore, I can host unlimited websites by create add-on domains. Wouldn't it be disorganized if I built a website on the main directory for that main domain, then build several other websites on add-on domains? Add-on domains are added as subdirectories in the main directory.

So, the reason why I ask this is, how do people organize their cPanel? Do they leave the main directory alone, and just focus on the add-on domain directories? I'm probably not using proper webhosting terms so I hope I'm not confusing anyone