It does not matter what port you use and there is no difference between the two. They both operate at the same speeds.
The purpose in having two separate LAN jacks is to provide you with what is called "multihoming". Basically what it means is that you can plug a single system into two other separate devices. For example: Let's say you want to plug two computers into a router that only has a single port. With this, assuming you share your internet connection to the second computer, you can plug this computer into the router, and then (with a crossover cable, of course) plug this computer into the second computer to share the internet connection.
Other uses include using a router for the internet and a switch to a local network, or two separate LANs via switches.