Ok the scratches can be taken care of by polishing. Some detail shops will add touch up paint to your rock chips then wet sand smooth then polish the whole area. It won't be as noticeable but if you want it perfect I'd say get the whole hood sprayed again....It also depends how deep those scratches are. As you know the process of polishing is to remove a thin layer of clear. My advice is to go to a detail shop and ask if they can fix those scratches. Worst case they tell you no, then it's off to the paint booth