I would say if you want only fish, the protien skimmer isn't necessary, but it is a major PLUS!!! You should see all of the stuff it pulls out of my tank, and i have a fish only. I can't imagine what my tank would look like if i didn't have one...
When i setup my tank, i added the water, then let it run for a day (to make sure it's properly aerated & the salinity levels are good), then i added the LR FIRST, and the sand SECOND!!! This is important. The LR should be on the bottom of the tank, and then add the sand around it. You don't have to add all of the LR before the sand, just the pieces on the bottom. This make your system much more sturdy. If you eventually get a fish that burrows, you'll be happy you did this, as burrowing fish + LR on sand = a lot of falling rocks, and possibly squished fishies... don't want that. You can add the LR and sand all on the same day, just put the LR first.
Also, i have a 2" sand bed. This is perfect for your display, i think, but this is a controversial matter. Some people say a deep sand bed (5-6"), and other say a shallow(2-3"). Here's what's up with that. A deep sand bed (DSB) holds more of the bacteria that processes your ammonia, and therefore keeps your levels in check. However, a DSB holds the nitrates in, and therefore, if it is stirred or moved, it will release those nitrate pockets, and cause a spike in your nitrates, which can be potentially deadly. For this reason, i chose to keep a shallow sandbed. As long as you have enough filtration, you will be fine with this.
Just a quick question, what type of w/d filter do you have, and what's the rating on it (meaning what size tank is it designed to filter)? I have a 55 gallon tank as well, and my w/d is a 75 gallon filter. This makes sure i have enough filtration, as a 55 gallon filter is adequate, but a 75 is much better (and allows me to keep more fish)!
Jenn