Those bolts should be most of the way in, in most cases. If they are sticking way out in the back, they can easily get bent, and the wheel may be too far back in the drop outs. They are there so you can adjust them to center the rear wheel. When the rear wheel is pulled into the dropouts, you want it to be perfectly centered. They make setting the wheel quick and easy. When you loosen the quick release and pull the wheel back so there's even pressure on both those bolts, check for how the rim is centered between the chain stays (by the seat tube). Adjust as necessary.