Nginx is pretty easy to set up. Look up “nginx virtual hosts”. You might want to use certbot/acme if you don’t have SSL certificates for your domain names. You need either a wildcard certificate (*.example.com), a certificate with SAN (Subject Alternative Name) containing the second subdomain, or two certificates (one for each subdomain). Note that subdomains can be found more easily than path based websites, if you allow connections from the whole WAN.
Files could be decrypted by the end user. The OS itself could remain unencrypted.