I usually call around to the local shops and tell them what I need done, according to the manual. They quote me a price. I've never paid more than a couple hundred bucks for the full routine. If you go to the dealer, they'll charge you msrp for everything (including the oil change)
As far as the tonneau cover goes, don't pay more than $630, if that's what the real cost was. If they want to charge you more, then tell them to shove it up their a**. Have you asked 4churchill or partsguy? I stay away from the dealer except for warranty work.