I moved the cert and key to a different directory and issued the commands below, it seems to be working fine now
/sbin/e-smith/config setprop modSSL crt /path/to/certificate
/sbin/e-smith/config setprop modSSL key /path/to/keyfile
/sbin/e-smith/signal-event post-upgrade
/sbin/e-smith/signal-event reboot
I would still like to know how to use the auto generated key if there is an easy way to have it put the domain name without the server name.