My D180 has a focus light that works pretty well, I find it helps a lot when shooting macro.
I have a varity of cards. Mostly I shoot 256 and 512 because that's what I have. 1GB's were not around when I was buying cards. If you are shooting in raw mode then by all means get GB cards because raw takes up so much memory otherwise I don't see the need to buy them. I would prefer to have several 512s and swap them when I have to change batteries. If one of them dies, I still have some pictures. How much storage you need depends on your opinion of what resolution is good enough. So far SHQ is fine for me.
I keep the magnet IN the strobe. I set it to auto and match the F-stop setting on the strobe to the camera's F-stop. Depending on the subject, how reflective it is, it's distance and ambient light, you may have to change the F-stop either on the camera or the strobe. I find it a lot easier to use the one on the strobe. On a shot I really want and have the time to shoot several I will bracket the shot by an Fstop or 2 on each side of the "correct" F-stop. Like I said before, if in doubt and don't have the time, guess on the under exposed side. I don't know about the D2000 but the 180 has labeling that says "Lighten" and "darken" under the strobe F-stop markings. You can play with this on land. The distances and F-stops will be different than underwater but you can see the effects of changing the distance and F-stops.
You can make the stobe fire at 1 with no problem. You may want to consider making a mask for the diffuser that you can remove underwater. You need to block the internal flash on most shots but I find using it along with the D180 on macro shots helps light the subject better. The main strobe coming from above and the internal stobe coming head on to the subject. When using both strobes in this manner, you will have to adjust the interal strobe for the best lighting, again error on the dark side.