Hi,
Port 2 will be a seprate device in callmanager.
If you have auto-registration turned on, connect a phone into port 2 and go off-hook. Call A IPPhone, see what number it has and you can find it back easily.
If you do it manually, add a ATA, but you have to shift the mac-address 2 digits to the left and add 01 at the end.
Example;
If the MAC address of the Cisco ATA is 00070EA26032, then the fabricated MAC address for the Phone 2 port would be 070EA2603201.
quoted from;
http://www.cisco.com/univercd/cc/td/doc/product/voice/ata/ataadmn/sccp3_0/sccpach4.htm
Make sure you have bought 2 licenses! If you only bought 1 license (End-point) you must disable the 2nd port....
HTH