People here would tell you to not paint it based on resale worries and what not. They'd paint over it with a brush to somewhat conceal it but make sure that they can say it wasn't repainted (but that still leaves visible damage).
Most proper professional way would be to paint the whole bonnet, which allows the whole panel to be the most consistent. For a few stone chips that would be absolutely overkill though.
The next best way then would be to remove all paint from the affected areas and layer all the paint and clear coat again and then polish it out to be as even as possible. You definitely would not be able to tell there was anything without super close inspection
