After every ispconfig update, ispconfig removes my certificates from main.cf and replaces them with the generic, self-signed smtpd.key and smtpd.cert. Any way to prevent this except symlinking the proper certs to smtp.* certs ? Any text field I can say, take this cert for the mail server. Same is happening with the dovecot configuration.
Do not change your main.cf file, instead replace the cert file content of the certs generated by ISPConfig.
And for a third solution, you could use a conf-custom template to specify a different smtpd_tls_cert_file and smtpd_tls_key_file. (Either of the other two would likely be preferred as you don't have to maintain a custom template in future ispconfig updates.)
Thinking it thru after your answers, I guess a symlink is the most hassle-free solution. There is a reason/problem I have with symlinks because I have the certificate creation/renewal/removal in a custom developed solution and outside ispconfig. That said, yes, symlinking will save me a lot more time in the long run.