best way to repair twin scoops

I agree with @72bluNblu that any decent filler will work.
If the pits are no worse than what I see in the picture, I would just use a good quality glazing putty (some call it a spot putty. It usually comes in a tube. It is a bit thinner than regular filler; it would probably spread on easier and fill the pits easier, and it sands easier than regular filler.