Ok, so if I read this right, you're looking to have the main Ip and the extra IP sent to the user correct? If that's the case, you should only need to edit the welcome emails from inside of WHMCS and include the variable settings. For example:
Main IP: {$service_dedicated_ip}
Additional IP addresses: {$service_assigned_ips}
As Cableguy pointed out, you should really be checking this on the WHMCS forums as it's all documented there many many times.