You want your skimmer and pump to not pull in any sand, so barebottom. If your skimmer needs an optimal height, most do, you may need to raise it with a stand so that it will sit at the correct height in the water. For the refugium there's lots of options, christy's got a few great thread's on them in the reference section. I use a 4" Deep Sand Bed and have cheato and a red grape algae, there's lots of options available.
Check out melevsreef for sump idea's, I'm building one of his right now and seems like a great setup.
Melevsreef