1. Yes, you'll want to add any organic matter in the same way it would happen without human intervention. All the material would just fall on the surface and the various creatures responsible for decomposition do the rest. Keep in mind that those creatures can only do so much at a time, but they are well-equipped to build soil from what drops to the ground.
2. There is another thread somewhere on these forums about the fruit trees. To apply his method, I believe you'll need to find trees that not only have never been pruned, but also that have never been grafted. Once grafted or pruned, a tree is dependent upon you for constant care throughout its life. Trees in untouched forests grow happy and healthy without people hacking off limbs or stitching together various parts. Fukuoka simply applied that to his orchard and made a fruit forest that never needed pruning. But if you try that on a tree that's already been cut or altered in some way, you run the risk of killing the tree.
I heard that Fukuoka just planted a perennial crop of clover and cut down the small areas for plants to grow in. By the time the plant has taken, the clover comes back and restores what damage you have done. Also by stressing the clover, you're getting nitrogen pulses that your plant can absorb.
I'm going about it that way, I'll report on any success.