Betti,
I just spent a few weeks in Indonesia, and in general I got the best WA results with fairly high shutter speeds (125th - 160th of a second) and medium range apertures (f6-8) rather than slower shutter speeds and smaller apertures (f11 or higher). If you are shooting sunbursts (even if they're behind the main subject), however, you'll want the shutter speed as high as it will sync with your strobe(s). In all cases, use your camera's meter to choose a combination of shutter and aperture that the meter says will underexpose the shot by about 1 stop.
As for the Magic Filter, I'd suggest that you only even ATTEMPT to use it on dives where you have bright sunlight and are in fairly shallow water. All digital cameras need lots of LIGHT, and murky water and/or clouds are likely to produce disappointing results with the MF relative to strobes. OTOH, if you're shooting a wreck or something else that just isn't practical for strobe lighting (so you have to use ambient light anyway), you'll likely find the MF produces better results than just having a blue water shot.
Hope that helps! Have fun; Palau is a beautiful place!