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.
You are on the right track. JB Weld is great stuff.
However, while building my Jango, I quickly encountered the same problem.
What you want to get is JB Quick. Made by the same company and probably sold in the same area.
This stuff lives up to its name. Only mix up what you can use fast, at it sets up, well, quick. You will have about four minutes from the time you finish mixing until it begins to set up and becomes unworkable. It gets quite warm while its is curing (exothermic reaction between the two part mixture).
I have found that mixing it on a plastic plate with a plastic knife works great. Just squeeze out the amount needed, mix with the knife and then spread into place. Maybe put it on a little thick and spread out beyond the are that you are working in because you'll want a little extra so that you can taper /feather out the area once you go back to sand it. Make sure that you wear a dust mask when sanding, you DO NOT want to inhale the dust. Nasty stuff. Then prime /paint or cover with good old Rub-n-Buff.
Sorry if this is long, but I wanted to make sure that my first post was helpful.