Tony, you'd like the entire rig, both truck and trailer, to be sitting level when hooked up. It's possible the dealer said to use the 3rd link because they had already checked the adjustment and found that to be the proper link. If not, once you get everything adjusted properly one time, then in the future you do simply use the same link in the chain (unless you have a pretty drastic cargo weight change). And yes, once you attach the trailer tongue to the hitch ball, then raising the trailer tongue does two things: (1) it makes sure they actually are coupled together, and (2) it makes it much easier to hook up the spring bars.
With a one ton truck, I'd say that must be a heavy tongue weight on that trailer for it to drop the rear of the truck 4". Normally, with properly adjusted weight distributing hitch, you want to drop the front bumper almost as much as the rear bumper of the truck; assuming of course that the truck was sitting level without the trailer. You might drop the rear of the truck an inch or so more than the front, but not much more than that.