Packets bound for the Internet will be sent to the port at the top of the list in System Preferences > Network.
There are two ways to use the other port:
1) assign it a fixed IP Address and connect it to different equipment such as Network Attached Storage.
2) Turn on Ethernet Sharing on the second Ethernet port and allow other Macs to connect through you to the Internet. Ethernet Sharing turns your Mac into a DHCP Server and can provide service to multiple connected devices.
I believe you can manually set the bit rate for the second Ethernet port when it is operating as Ethernet Sharing (essentially turning that port into a limited Router).
There are no standard tools in Mac OS X for inspecting the packets there, but there may be tools available for networking developers/troubleshooters to do that.
When that feature is enabled, the port appears from your Mac to have a "self-assigned" IP Address -- a semi random Address in the 169.254.xxx.yyy range. From the connected devices, it will appear to have a legitimate private Router Address, often 192.168.1.1