The skin feature was mostly made for us developers to try different graphic styles. It is not complete so you can't fully change the look of the game. We might improve it later on though to make it more user friendly and let people upload and share their skins. It will however not come in the next update.
Building a new data.jar file can give you a problem when the game updates itself. Likely the update will fail and you'll have to download the game client again.
Still if you want to work on your skin I suggest you do as you've done now. Replace all pictures in the "images" and "skins" folder in data.jar. Please send the skin to me when you're finished. I would love to see it
