Don't put the glass tops on the tank. Your corals will receive alot more of the needed light without the covers, There are also heat issues, and gas exchange issues.
If you are thinking about getting fish that might be jumpers, or you feel better haveing something over your tank, use the eggcrate.
As far as the lights on top of the tank, you will not sit them directly on the tank, you will need to use the legs that come with, or you can order for your light. The other option it to hang the lights from the ceiling. Alot of the lights do offer hanging kits. You will want this space between your lights and tank for a couple reasons, one being the gas exchange, and two. So your tank doesn't heat up too much. If your tank is still too warm, then the space is also large enough for a fan to blow across the top of the tank, and push the heat away.
As far as the box saying not to put on open tank, or your should have glass over the tank, That is not so. I have seen a lot of different light fixtures, and almost all of them come with some sort of clear plastic cover for the lights. This alone will protect the light from moisture. Also your light will be at least 4inches from the top of the tank. I've seen alot of filters and skimmers throw water back into the tank, but I do recall it throwing water so hard that it splashes 4inch out of the tank.
So in reality all that is going to end up on the lights is salt dust. That isn't going to hurt anything, except getting the light shield a little dirty. I don't know about most others, but even when I was new also and had glass covers on my tank, my lights still got dirty with that salt stuff, so as far as that goes, the covers don't do you any good.
Just make it part of your weekly routine to clean the light shield every week. All you do there is get a towel, table cloth, just something large enough to cover the tank, put it over the tank and then just get a damp cloth and wipe down the light, all the crud will fall on the towel. When done just pick it up, and shake it in the trash.
Try not to let alot of the salt stuff fall back into the tank, It could be enough to raise your salinity.