The easiest way would be to set up caddy to use acme on the servers, and never care about certificates again. See https://caddyserver.com/docs/automatic-https.

If you insist on your centralized solution, which is perfectly fine imo, just place the certificates to a directory properly accessible to caddy, and make sure to keep the permissions minimal, so that the keys are only accessible by authorized users.

If the certificates are only for caddy, there’s no reason to mess around in system folders.