Each valid website or a VHost when setup properly i.e. the IP address of the website should point to the VPS, will have its SSL certificate automatically configured at the time the website is added or later (on scheduled intervals) when its IP begins pointing to the VPS. The free certificate is issued by Let’s Encrypt and is valid for three months. ideally this certificate is automatically renewed within three months, but for reasons like wrong IP pointing etc., it can get delayed or may not get renewed.
In the case where you have purchased a SSL certificate, you can have it configured from N99panel console.