Here's my recent experience (less than two months ago):
1. Empty gun goes inside an approved, locked container (this container does NOT need a TSA approved lock).
2. Ammo can go inside same container, as long as it's in a separate box (like an ammo box)
3. Magazines can also go inside same container.
4. Go up to check in counter, show your ticket and ID, tell the clerk - I need to declare a firearm
5. They will have you open your bag and show them the gun. They will ask you if it's unloaded, Say yes. Offer to demonstrate that it is. Clerk will recoil in horror and say no, that's ok.
6. Sign the orange tag they give you declaring an empty gun.
7. Orange tag gets affixed to gun case or put inside gun case (depends on the clerk I guess)
8. LOCK your guncase.
9. Zip up suitcase and lock with TSA approved lock.
10. Airport clerk will escort you to the TSA bag x-ray section and will inform x-ray screeners that you have declared a firearm
11. Hang around x-ray area until they are done with your bag. They might look at it on the screen, then let it go. (happened twice to me) Or they might pull it out (using their TSA key to get into bag, then asking you for the key to the gun case) and call everyone over to look at it and make you worry that someone's going to walk off with one of your shiny Mec-Gar mags (happened once). They will tell you when they are done and everything's ok.
12. Go through regular security like everyone else
13. Pick up your bag when you arrive, go to a discreet place and make sure your stuff is still there because you're paranoid (happened 3 times)
That's all there is to it.
The responses I got from the airline people when declaring a gun:
1. Salt Lake City: Oh, ok.
2. Ft. Lauderdale, FL:
A gun? Oh, let me find out what to do.
3. Kansas City: [mild shock], Ok, let me find the proper form.
From what I recall, you CAN NOT use the skycap service to declare a gun - you have to go to the counter.
Edited to add: I was on Delta.