Use the spacer. Once you tighten down the nut the rear bushing seats appropriatly.
You can run without the spacer, its purpose is just for positioning. If you remove the spacer then your front axle might not be positioned in the center of the wheel well, it will be short of center. In my experience while putting on the 6 inch SJ kit, my axle was still back from center even with including the spacer. Therefore i added one of the black factory bushings behind the large front bushing. (if you start from the front of the truck, the smaller original black bushing would be the first in the series). You may or may not want to do this, its just sort of a pain in the butt to adjust the front bushings after everything is put together.
Also, while tightening the nut on the radius arm, make sure to put a strong hose clamp around the white plastic spacers. Both of mine cracked while tightening and i had to order new ones from moog, maybe i just tightened them too hard but idk. If you run with a cracked spacer then you will get an annoying clunking when braking hard because the radius arm is slipping back and forth.