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Oh certificates are so much fun and you have so many options. From fairly easy to mindboggling complex.
Your current solution is OK if you keep in mind security implications of distributing certs using scripts.
It is not entirely clear where you do your tls-termination but it sounds like that is the Caddy reverse proxy so that is where your certs should be.
Placing them in a location like
/etc/ssl/example_com/asfullchain.pemandprivkey.pemis probably easiest. Make sure access rights are appropriate. Then point Caddy at them and it should work. No experience with Caddy itself. If Caddy runs in Docker be sure to map the certificates into the container.Mind that in this scenario the certificates are only on the Caddy server, connections from the reverse proxy to the services is unencrypted over http. You can't easily use the LE certificates on the services itself without some ugly split-horizon DNS shenanigans.
Alternatively you can set up a PKI with certificates for your services behind the reverse-proxy for internal encryption and do public tls termination in the proxy with Let's Encrypt.