Skins are alternative images for specific Lieutenant. So far, they have all been awarded during, or for achievement in, Events. If you open the lieutenant, you'll see arrows allowing you to page sideways to any skins for that lieutenant. If you're looking at your lieutenant, it will specify the criteria to unlock the skin and provide an "Unlock" button. Skins have no effect on gameplay.
Support for skins was added with the 1.76 version of the UE client.