Trying to fill scratches with paint doesnt work very well, especially if your using 1k, tends to follow the scratch and trasnfer it through, cant judge without seeing it but if you have the primer based then keep sanding, if not chuck some more primer on, or if your using 1k you can hit it with 2 coats of colour, then sand with 600grit, hit with a 3rd coat of colour or until hiding then clear.
If you just paint over them, more than likely they will be magnified.