Hi there,
The typical paradigm would involve installing a control panel on the server OS to provide systems to interface with the server for provisioning and managing the accounts on all the various systems. That control panel provides an API for systems like WHMCS to communicate with.

That said, a provisioning module could potentially be created to SSH to a server and perform the various management directly in the OS. There are PHP functions which make this kind of thing possible such as ssh2_connect or phpseclib.

The documentation for creating a custom provisioning module is located here: https://developers.whmcs.com/provisioning-modules/