I don't have a lifted truck, so I cannot adequately asnwer your question on that issue.
I know it may not seem helpful, but allow me to ask a few questions regarding your question. That might better allow you to understand.
Are you in a position to buy, or have you already bought, one model versus the other? The 2500HD and 3500 HD are similar, but not the same as far as build criteria. The old addages of "1/2 ton, 3/4 ton, and 1 ton" refer to the 1500, 2500, and 3500 series, but they are not truly a representation of the carrying capacity that they once inferred.
Are you concerned about actual payload capacity (what you would carry in the back)? Are you more concerned about towing capacity (what you would pull from a reciever hitch)? A combination of both (such as a 5th wheel/goose neck)? How well do you want it to ride? How often would you have it loaded near capacity? These all weigh into your decision.
Also consider that the 2500HD and 3500HD are equipped differently when it comes to the support systems. Usually, but not always, there are different bearings, bolts, springs, spindles, wheel sizes, and even frame thickness dimensions that all play into the capacity ratings from the manufacturer. Sure, the two trucks look the same, but are they actually the same? The manufacturers rate them differently for a good reason. The two trucks do come with different rear differentials; I can assure you that the don't just do this for the fun of it, they are rated for different capacities for a reason. The bearings in the wheel packages most likely are uprated for the heavier truck. At one point, I remember that you couldn't get 265 tires on a 2500HD, and many people wondered why not. Well, larger wheel/tire packages place different stress levels on the associated components such as the bearings, spindles, caliper bolts, etcetera. The list is nearly endless. I know for a fact that Ford rates its F series superduty's in a progressive fassion because the actual frame section thickness is different as you go up the line (comparing F250, to F350, to F450) even though all the frames appear to be made the same. You see, they use the same body for the superduty series, so all the body mount locations must be the same, but the load and pulling capacities are different based upon the actual components built into the vehicle. The axels are sized diffently, the bearings, and ring gears, and so on. I can assure you without a doubt that the GM products are engineered the same way. The farther up the series you go, the heavier the components get based upon the expected capacity ratings. For some components, they do use interchangeable parts because they are deemed more cost effective to use one for multiple applications, but the towing/carrying/pulling items such as frame, bearings, wheel size, axels, etc are size for an application. The applications sometimes even overlap. A 2500HD with a snow-plow package might be as "beefy" in the front end as a 3500HD, but not so in the rear.
To truly get the answers you might desire, you'd have to get the "spec books" that actually define the components involved, and you'd see that there are some siginificant differences between the trucks. These are what aftermarket companies use to build up vehicles such as RV's, emergency vehicles such as fire/rescue trucks, and industry trucks such as you would see plumbers/carpenters using with aftermarket beds on them.
Now what you need to decided is do you need a 2500HD or a 3500HD? The ride is not as nice on a 3500HD, but it can take just a bit more in most catagories. Also consider that if you are going to be near the limits of the 2500HD, you might feel more comfortable with the capacity buffer by stepping up to the next level in a 3500HD, giving you some piece of mind in not overloading/overstressing your truck. Or if you don't really need the beef of a one-ton, how much do you really want to bounce around when empty?
Don't forget that when it comes to maintenance, such as tires, bigger costs more too.
I bought a 3500HD because I don't use it much from day to day. I use mine to pull a travel trailer. I bought mine off the lot, as a left over 2006 model, and got a great deal. I really wanted a 2500HD CC with a short bed, but I setteled for a 3500HD with a long bed because I couldn't pass up the deal they made me, and it was hard for me to locate what I wanted at the time, and I looked around a lot.
If you are honest with yourself and decided how you're going to use the truck, you'll be able to get what best suits your need. Or you might be like me and decide to alter your decision based upon a great deal that would sway you in another direction.