NMoasis said:
You don't say how big the rocks are, but if they were small enough to shovel with the dirt, they won't bother most plants except root crops... they get misshapen in rocky soil.
About composting in place: that could get messy and counterproductive unless you plan to let the compost cook for about six months before planting. Spot composting in larger inground gardens can be effective, but I'm not sure about a combo compost pile/raised bed plan. Maybe I don't understand what you have in mind.