I recently took an REI class on how to pack a backpack. They recommend compressibles (sleeping bag, clothes) in the bottom (because the weight of the rest of your gear above will compress them even further), then heavier items like sleeping pad, food, fuel, cook system, etc. in the middle, and finally on top any items needing easy access like toiletries, first aid, snacks, rain gear, etc.
That said, a pack like the Zpacks Arc Haul Zip throws some of this advice into question since you can access nearly all your gear simultaneously via the main zipper (or use the outer compartment as a substitute for the "brain"). But the basic concept of weight distribution still holds true.