First of all, it's CE, not SE. Secondly, the differences are decribed right on the main page if you scroll down enough. Jesus.
"The X3CE has also started to ship to resellers. Basic differences are similar to the X2.6CE - a better connector of the alt 5v point as per requested by our users, a 90 degree angle IO socket for easier install / positioning of the No Solder X3LCD screen as per requested by our users (you ask, we apply), a different design flash protect switch now with LED to give a batter indication of flash protect status, better layout of the I/O solder positions / points and also the different colors that correspond with the current CE design (white front, red back). There is no functionaility difference to the original X3 - it is simply a couple of tweeks to the hardware layout - the original X3 (Purple PCB) will function exactly the same if you have bought one of those so don't worry if you have the opriginal version it's general functionality is the same."
Look there for screenshots.
As for flashing, go here:
http://home.comcast.net/~x3guide/