Melissa, if I read your post correctly, you have a plain vanilla cover, maybe something like the one below?

If you are going FOWLR in a 55 (18" deep, right?), you need to make sure you have good flourescent lights in that hood (50/50 type). This will give you some limited coralin algae growth on your LR, but in 6-9 months these types of lights will degrade and need to be replaced to keep undesirable algae from growing. If I'm right on your lighting, you don't need to be too concerned about heat and evaporation due to the tight fitting cover - but you will need to deal with saltcreep and probably weekly cleanings to keep the glass panels under the lights clean.

Starting out simple (and less expensive!) is fine, you will learn a ton from your first tank! This setup won't support corals, well maybe a zoa or two up high closer to the lights.

Your airlift skimmer is gonna be a challenge to place through this type of hood. CD's eggcrate idea might work, but some clever cutting and fitting will be needed - buy lots more than you ned so you can make a few mistakes.

Is there any chance that the skimmer would fit in the back of the HOB filter? Or are you mechanically talented enough to add on a chamber to the HOB to house the skimmer? That would be tricky, and you would ned to push water from the HOB to the skimmer chamber and back again.

Hope this is helpful ... not meant to be confusing.

Good luck, and enjoy your first SW tank!