How deep are these "low spots" you are talking about? Are they pits from rust or just stamping marks or what? If they are not deep (say, about a 1/16") you could just prime it with polyester primer to fill them. This is much easier than spreading plastic filler and sanding. But, if they are a little deeper, you could fill them with the body filler THEN polyester prime to fill the smaller things and sand to perfection. The etch can be sprayed after body filler, it depends on the brand you are using and the part number.
