Original JB Weld, the red/black/white package, is indeed messy, and is not intended to form a putty-like substance. When mixed in proper ratio, one part to one part, it should turn a uniform grey color. It takes a few hours to set, and usually hardens overnight. The great thing about JB Weld...it dries hard as a rock!
If you're looking for someone with more of a 'putty' texture, I recommend Plumber's Putty, available at most hardware stores.