I have a flashlight attached by a lanyard to my left shoulder D-ring; during the dive, I swim around with the camera rig in my right hand, and flashlight in the left, scanning the water around me with the beam. The camera is set up with two strobes, one on each side of the lens, pointing forward and inward, plus a focus light on top, pointing forward and down. When the beam highlights something interesting, I get closer, bring the camera in front so that the subject is illuminated by the focus light, drop the search flashlight so that it dangles on its lanyard, and use both hands to get the subject in the frame and in focus, which is more difficult than it sounds. My lens of choice for this is Canon EF-S 60mm macro on a Metabones IV adapter. Some subjects ignore the light, some are scared by it - in that case, switching to red mode on the focus light sometimes helps, although it makes framing even harder - and others are attracted to lights, in which case it helps to turn off the focus light and use the modeling lights on strobes for focusing; this way you don't end up frantically backpedaling away from a critter that's trying to bump into your focus light.
Some more blackwater pics.
Filefish eating a jellyfish
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Swimming crab
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Squid
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Radiolarian colony
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Jellyfish
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Salp chain
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Juvenile black pomfret
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Some kind of filefish, I think
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Juvenile trevally
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I just found out though that a work project getting rescheduled will cause me to miss a dedicated blackwater liveaboard trip this January which I signed up for way back in May