The luggage rack is hard to fill, even for an expert, because the deck is so large and flat, the hole fill spots tend to come back over time.
What I mean is, the body filler material will shrink as it cures and it will continue to do so after the car is repainted. This will cause little dimple/imperfections/rings around the holes where the rack was installed.
To avoid this, you must take your time, use good quality materials, and make sure the deck can sit out in the sun, or under a heat lamp while working it to cure it 100%.
To fill it, you first grind the hole so that it has a creator effect. Now, you can tape from the bottom. One method is to use chopped glass in small pieces, and fiberglass those down in the recessed ground out hole area. Let that cure (note above--heat lamp, sun).
Come back, grind down the high spots, and rough the whole area up. Now, using standard filler, mix it and spread it into the repair area.
You want to use a 17" air file, or simply a 12" or so block of wood with a long piece of paper to hand work the area over a large section of the flat surface. Using a large sanding device over the small area keeps you from digging down while trying to smooth it. What you want to do is lightly fill the whole area, then slowly bring it down with decreasing grit paper.
Finally, use micro thin filler (putty coat, icing, etc--see your auto paint store rep for the best two part product). Fill in all the final small sanding scratches, pits, etc.
Next you want to use a two part primer (urothane is best in my opinion). Prime the area, let it dry, then block it using a nice long flat block.
Contiue the prime and block until it is looking good.
Heat lamp, sit in sun.
Next get some guide coate....or just some laquer black spray paint and dust it over the repair spots. Let it dry, and wetsand block it out. The goal is to use that guide coat to sand and make sure there are no low spots.
If you have time now, let it sit in the sun for a week, and come back and do it one more time, then one more time before painting and you might...get it to go away.
Hope that helps.
Paintdaddy could be of more help if he sees this thread.