Experts and BHG readers answer.
Though it would be a big job, the best thing would be to dig out and replace some of the rocky clay soil with fresh topsoil. As another option, you could build raised beds or berms to plant in and simply cover the soil's surface with a foot or so of fresh topsoil mixed with organic matter. In the time it takes the added soil to settle, you can plan what you'll plant. If adding loads of soil isn't an option, you'll have to rake or pull the stones. Once you have removed enough of the stones to easily work the soil, amend it liberally with organic matter (such as compost) to loosen the clay.