This is a very broad question, as there are thousands of different virtual hosting providers, all set up differently.
If you have ssh access and access to the http config / ssl folders ( as the OP) then you have the option of most of the clients personally I use ACME Tiny
Most Virtual Hosting providers have a “control panel” which you use to input the certificate information ( e.g. cpanel, plesk, ISPconfig etc). Depending on which of these it is affects which client you would use. Sometimes the easiest is to talk to your hosting provider and persuade them to include it in there offering ( they can then integrate LE with their control panel ) .