Hold your smartphone or the sensor for the lux meter at the water line, facing straight up at your lights. i.e. The sensor will be "looking up" with a line of sight perpendicular to the water surface.
Mostly you're interested in finding your maximum lux reading and discovering how large an area of your water surface that maximum covers. So just glide your phones/sensor across the water surface until you find your hot spot (or spots, depending on your lighting) and then you're started!
You might also be interested in defining your so-called L80, L75 or L50 areas - or where light levels fall to 80, 75 or 50 percent below your measured maximum.
If you're curious about what light a particular coral is getting, just watch the shadow your phone/sensor throws on the rocks/coral below. You are sampling the light (more or less) that would normally be hitting that shaded spot (and the coral, or whatever is in it). Makes sense?
FWIW, light levels beneath the surface are highly variable under actual day-to-day conditions and is why I don't worry about trying to measure there. If you want to know the actual lux reaching a particular depth, just calculate it mathematically. It will be an "ideal" approximation, but that's all we're dealing with anyway - good enough.
Last, I really wouldn't worry about converting to PAR for your own needs. You'll be fine dialing in to the natural target ranges of
"overcast", "full sun" and "direct sun" and gauging with your lux meter. (If you needed to compare with someone else's PAR readings conversion may be worth it, but that's not really the case here.)
-Matt
P.S. There're only about 4 hours or so of peak light levels in the tropics. If you have the lights up to direct sunlight levels (per the lux meter) keep this "time limit" in mind and make sure the ramp-up and ramp-down periods are pretty dim.