Top-down photos can be challenging. I'm not a big fan of photo boxes because the acrylic you shoot through is not of optical quality and scratches easily. Photo boxes are also hard to hold still so it's difficult to get sharp images. My personal dislike is based on the fact that I'm convinced that I'll get so involved in my photography that I'll forget what I'm doing, move in for a closer shot, and flood the box with saltwater. That's never a good thing.
If you're going to use a box, I suggest Marc Levenson's design (melevsreef.com). He has a good understanding of photography and I think his box design is probably the best.
As for top-down shots without sticking your camera in the water (you didn't say, but I'm going to assume you're using a DSLR), you need to have your camera on a tripod. Note: Please be very careful doing this. I find that if you lean your tripod against the tank/stand and extend the tripod column, you can get the camera out over the water so you can aim the camera straight down. It's essential that the face of the lens be parallel with the water surface.
Turn all of your flow off so your water surface is as calm as possible. Composing and focusing can be challenging because your camera is face down. Your LCD screen can be a big help. Your problem is eliminated if you own or can borrow an angle finder to put over the eyepiece. Either way, with the camera facing straight down and the photo composed, photographing is straightforward.
Now for the challenge: Light reflection. Yes, it's a pain. If you can, move the coral near the edge of the aquarium. You'll get calmer water and be able to shoot without reflection. If the shot you want is where the T5 lamps are reflecting and the fixture is resting on the tank, simply move it to the back. If it's hanging, have someone tilt the light away from you until the reflection is out of the shot. Yes, either way you're giving up light, but the coral isn't going anywhere, so just use a higher ISO setting and/or slower shutter speed. If you're on a tripod, you'll get the shot. If you shoot in RAW and have the proper exposure, it's simply a matter of adjusting the white balance to get the look you want.
Sometimes, if you have a nearby window, you can have some fun on a sunny day by turning off the tank lights and using light from the window to light your tank.
Let me know if you have additional questions. Here are a couple of shots I made a few years ago with the camera above the tank water.
Gary
