I'm not quite sure what was meant here, but unless there is something special about your particular setup, the flash does not "stay on longer." The light burst of a strobe is for all intents and purposes instantaneous. The adjsutment for the intensity changes how much energy is discharged.
Let me preface this by saying I am an above-ground photgrapher that is jsut getting into UW photography. But I beleive all the following below still applies.
The way you determine the right settings to use has to do with something called the "Guide Number." This number is used to figure out, given a certain distance, what f-stop your lens should be set to. For now, as long as your shutter speed is at or slower than the "sync speed," we'll ignore it.
Underwater, the effectiveness of your flash is hindered by the light blocking characteristics of water. So look in your camera manual specifications (or strobe specificaitons) for the guide number. It is basically a "length" measurement, so will be specified as feet or meters at 100ASA. Divide that number by 3 to get your underwater guide number For this example, lets say it is 15 ft @100ASA. Set your "ISO speed" on your camera to 100.
Now, when you are underwater, think about how far your subjects will typically appear. Remember that the water magnifies. Let's assume that things will appear to be 3 feet away.
Divide the Guide number by the distance (15/3) and you get 5. Voila! Your f-stop should be 5. (Actually, 5.6). In reality, you'll have to experiment a little, because the guide number is probably not 100% accurate. But that's the great part about having a digital - instant feedback.
You can then look at compensating with the intensity adjustment if you want. Things are closer, reduce the intensity. Alternately, you can reduce the aperture (f-stop) (in photogaphy parlance, reduce aperture= make the number bigger, so going from 5.6 to 8 is reducing).
Now, getting back to shutter speed - how does that play in?
The flash will expose what is in the foreground, but the flash may not reach all the way into the background. When you see shots that are light up front but dark the further away you get, the photographer just set the camera to the max sync speed and left it there. In actuality, you probably want it slower than the max. For example, my camera syncs at 1/250th of a second. But if I do that, chances are my background will be dark. So I'll shoot with the shutter slower, so that more natural light from the background will get into my camera (thus brigtening the areas my flash couldn't reach). In general, you can shoot as slow as the inverse of your focal length without having to worry too much about blur due to camera shake. So if you're shooting with a 28mm lens, you should be able to shoot around a 30th of a second - maybe shoot at 1/60th to be safe.
This is why I said above that the strobe is for all intents an purposes instantaneous. The way a good photographer gets an action shot in low light conditions is to use the strobe to "freeze" the action (since it is instantaneous) and then they expose the background with the shutter speed. Ever notice how those shots of nightime football games are really sharp in the foreground, but kind of ghosty and darker in the background? It's becasue of this - the foreground got nailed with the strobe, but the background was exposed for a longer time period.
Hope that helps - and hopefully, all these rules really still apply underwater.
RiotNrrd