Rob, your harsh ride comes from the overload slamming onto its pads every time you hit a pothole - essentially you already have a decent ride from the main springs with that bed, but the overloads are messing it up for you. The way you describe the overloads current position it seems to me that it's the main springs alone that carry the weight of the bed empty, so if your current ride height is acceptable then I'd remove the overload leafs and install the air bags in their place - this way you lose the jarring the overloads cause when empty, but when you load up you can still lift the ass end of the truck to normal ride height with the air bags. If you remove a main leaf you will weaken the main pack, causing the ride height to drop some resulting in the overloads to ride firmly on their pads all the time with no air in the bags, which will make for okay ride but the moment you put air in the bags to restore ride height the overloads will be right back where they started - barely touching the pads and jarring the truck every time you hit a pothole. You see, it's more of a geometric issue at this point, the overloads are just not where you want them for a decent ride.
Now, if your current ride height is a bit low, you have a few other options:
a) install air bags on top of overloads, pump airbags some - takes the overloads off their pads so jarring is gone, but the overall ride is somewhat stiffer all the time
b) remove overloads, install air bags in their place, pump the bags up some - no jarring will ever occur, but overall ride will be somewhat stiffer all the time again.
c) remove overloads, move their 1" spacer blocks between the main springs and the axle perches, and run the air bags with no air in them - no jarring will ever occur cause no overloads, you gain an inch of ride height from the spacer blocks (now acting as lift blocks), and your ride is as soft as it can get cause no air in the bags. What you gotta watch out for this is if the air bags require some pressure to be kept in them at all times, cause if they do and you go with this option you may end up with the rear end higher than you wanted it...