How to use Let's Encrypt certificates for a service that already has a certificate?

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I am running proxmox on a server along with Nginx. I was wondering how I would use one certificate for local access and another certificate for access through Nginx.

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One possible answer to this (quite vague) question :

I have a setup with nginx in one container serving as reverse proxy. This is where I defined the Let's Encrypt certificates corresponding to domain names hosted on the containers served by the nginx one...

So certificates can be installed on the reverse-proxy container because it is acting as a front.

If your nginx is installed directly on the host, you would then install the certificates on it, no need to do that in each container. (As side note, the containers can be self signed)