When I make a raised bed, I also break up the soil under the bed and amend that, to whatever depth is fairly easy to break up. I'll go down 6-18 inches, usually, before putting up walls another 8, 12 or 16 inches high.
I'm careful to make the "floor" of the bed (unimproved clay, in my yard) slope down towards the lowest edge or corner of the bed, and make sure that edge or corner has somewhere to drain down into. Sometimes I have to cut a slit trench from the low corner of the bed to some lower spot in the yard.
That gives roots an aerated zone they can penetrate in search of minerals and water. As the roots penetrate deeper into the amended clay each year, they break up the clay, and enrich it with organic matter. But the roots won't penetrate deep unless you arrange for excess water to drain OUT, which lets air IN.
Really, when you aerate clay like that, you're lowering the temporary water table that forms in response to each rainfall or watering.
I figure that fertilizer and organics are going to be leaching out of the very good raised-bed-soil. If I have drained the deeper soil by breaking it up and amending it a little, that fertilizer and organics AND AIR will allow that deeper soil to attract worms and other soil life.
Over time, the root zone of my "raised" bed will become twice as deep as the walls would make you think. If the drainage is good, it becomes a raised and sunken bed.
