That's how I do it. Weigh the stuff sacks-- you may be able to balance it out.
My pack (GoLite Trek) has a hydration sleeve against my back, so the bladder goes in and does drop down to the lower half of the pack. I use a Z-Lite pad and that is arranged in two even columns which goes against the bladder. The stuff sacks all go up against the Z-lite. If I use another sort of pad like a RidgeRest or self-inflating, it goes in a circle wiht the stuff sacks inside.
I have one Sea-to-Summit waterproof bag with my sleeping bag and another with spare clothes, especially critical insulation. Hat gloves, windshirt and rain gear can stay up top or an outer pocket to make quick changes. Another bag is my ditty bag with essentials-- that really keeps things from spilling all over the place. My cook kit goes in a small mesh bag and I've teneded to throw that in a large drawstring sinylon bag with food that is also my bear bag-- trying to get all the smells in one place.
The sleeping bag goes in the bottom (I need it least) with spare clothing alongside. Food and essential bags are stacked above. The alternate layers like windshirt and rain gear go on top, or with my rig, in the top or front pocket. My latrine kit goes in the front pocket in a Alocksak or ziplock.
One nice advantage of UL geat is that no one item is so terribly heavy that it will really set you off balance. My sleeping bag (3lbs) and 2 liters of water are the heaviest components of my pack. The water is centered and the sleeping bag is large enough that two other stuff sacks nearly equal the weight and size, so it balances. Another solution would be to put the bag horizontally across the bottom, centering the weight and stacking the other items on top.
My setup with the Z-lite near my back makes me wonder how effecient the setup is-- I'm moving the weight out a few inches. It is nice and stable, but I may get better results moving the Z-lite to the front of the pack. I just wonder how much "frame" I will lose by doing that. Time to experiment!
Stuff sacks can add up. The Granite Gear silnylon bags are nice and the Sea to Summit UL silnylon waterproof sacks are great-- just an ounce or two each. I have a 13 liter for my sleeping bag, a 8 liter for spare clothes, a 2 liter for essentials, and a 1 liter for electronics and camera. I had some older Outdoor Research waterproof bags that were 3-4 times heavier than the Sea to Summit bags. I saved a good 12oz by switching.