The best way to go about it is to fill in the places that you're going to touch up, and using the paint and the clear coat, build them up higher than the rest of the car - so they stick out a little bit.
Let the clear coat dry.
Next, using some 2000 grit wetordry sandpaper, sand them down flush with the body, and 'feather' the repair into the exsisting clearcoat (just sand a little outwards into the clearcoat). You should have a pretty smooth area that follows the body lines and the repair will be flush.
Once sanded, use a tack cloth to get rid of the dust. Take out your orbital buffer, and with some fine cut compound (I use griots #3, I think, but it can be really anything - you can get some from the local auto parts store), buff over the area until the scratches are gone - this would also be a good time to use the fine cut over the entire car, while you have everything out, and get it back to a showroom shine. Be careful on sharp body lines, as it doesn't take a lot to rub off the paint. Also, make sure you don't press down on the buffer, just let it do the work. Use some good wax on the car afterwards, but you'll want to avoid waxing the part that you touched up for a month or so.