A picture would be really helpful, as I'm not sure my solution would fit with exactly what the situation is.
However, I have a simple wooden frame made of 2x4's with the 2x4's sticking out sort of like an "H" shape except two bars across, designed to fit over a wheel barrow. The center part is covered on the bottom with 1/2" hardware cloth - that's the square wire material that sometimes has other names depending on where you live.
So if I'm picturing the beds correctly, I'd use a garden fork to loosen the rocky stuff if it's settled into a mass, then use a shovel to put shovel-fulls into the shallow frame and the theory is that the dirt will fall through and the rocks will stay in the frame and can be dumped into buckets. Reality usually means that you have to rub the material around to get it to separate, but at least you're no longer doing so on your hands and knees.
If the main issue is that the rocks have settled into a solid mass, trying just the garden fork and not using the frame, may still be helpful. You may have to clear a strip in the center wide
enough to get the fork in to lift from under the rocks.
If I've got the whole problem wrong, post pictures and maybe we can do better?