You'd put the dedicated site on the 2nd IP and the 1st IP will be the shared server IP.
1) Add both IPs to the server (IP Manager)
2) Assgin both IPs to your "admin" account (IP Manager)
3) create a new User account to your your dedicated domain (so you can more easliy use ssl). Select the 2nd IP address and enable ssl.
4) go to Reseller Panel -> Nameservers and create the namesevers with the new domain. Use the 2 IP addresses.
5) Make sure the correct nameservers are set everywhere (bottom of the sceen in step 4) and also Admin Panel -> Admin Settings.