I don't have the upper either, but I also have lowering blocks with a tapered protrusion at the top to act as a locator into the bracket. Don't think the spring center bolt has a large enough diameter at the top to positively locate the leaf in the bracket. Maybe take the metal bushing out of the pads and put it over the top of the pin before you drop the rear over the springs.
They are meant to quell vibration, but most do not notice a difference without them. They probably don't do squat anyways once they decay, so shouldn't be worse than what you had before.
P.S. If you remove the upper pad altogether, it will raise the car the thickness of the pad. The lower will not affect ride height.
