We would highly recommend installing WHMCS on a sub-domain and keeping your website files on your main domain. An ideal setup would looks like follows.
1. For hosting your website and files:
my-domain.com ( public_html ) – Always host you website files on public_html folder.
2. You have few options for your WHMCS install as follows:
members.yourdomain.com ( public_html/members )
billing.yourdomain.com ( public_html/billing )
clients.yourdomain.com ( public_html/clients )
support.yourdomain.com ( public_html/support )
anything.yourdomain.com ( public_html/anything )
Installing WHMCS on a subdomain like above will help you to keep your WHMCS separately and will save you lot of time in the future when upgrading software, maintenance etc.
3. Creating the subdomain from cPanel.
Login to cPanel and go to Domains > Subdomains. This is where we would be creating the subdomain to install WHMCS. On “Subdomains” page you can create the subdomain from Create a Subdomain. To create the Subdomain you have to details on following fields and click “Create”.
Subdomain: Enter the subdomain prefix here, eg. billing
Domain: Choose your primary domain from the dropdown menu.
Document Root /: Documentroot should look like, public_html/subdomain-prefix eg. public_html/billing