Amending Rocky/Clay soil

I've got a very rocky layer in my garden (small pebbles, some rocks) for about 2-3 inches, then clay. Zone 6. I'm planting my garden and augmenting the soil manually around all of my larger seedlings (tomatoes, peppers, squash, etc). But I have a bunch of empty space that I figured I would just fill in with anything and everything that I could direct seed that could protect and enhance my soil for future seasons. So what can I plant for this spring/summer that will best help my soil?

Thanks!