Two ways of making it work. The old school way of stroking was to put a spacer plate under the crank to make up for the added stroke and keep it from smashing the piston in to the head/dome. There are several reasons to avoid doing it this way. First, you raise the ports up and it makes the motor come on slower. Second, the ports aren't totally optimized for the stroke, negating the benefit of stroke. Plus the plate adds one more base gasket which is another air leak prone area that will quickly melt a motor.
In recent years, guys have began setting up 4 mil strokers with the cylinders in the factory location instead of up on a plate. One gasket, or even just liquid sealant. Less prone to leak, and it keeps the ports lower so that the motor comes on a bit sooner. They adjust portwork for the desired ride style and cut the domes or factory chambers for fuel/compression needs. The domes are cut with a step to allow the piston crown to come up out of the deck and still not collide with the dome. This is the far more reliable and better running set up. I've got a few 4 mils on the bench and have tried several set ups and the non plate stuff always seems to live longer and hit a touch earlier if you're not doing a drag only set up.