While you may eventually drag ropes all over the reef (carefully avoiding contact with the reef, of course), for the first pass you can just use kick cycles.
This worked pretty good for a rather complicated shaped reef with a well defined sand to reef outline. I just did a series of straight line approximatons of the reef and recorded bearing and # of frog kicks for each segment. EG: 10k @ 240, 15K @ 200, 8 K @040, 4K @ 090, 12 K at 160.
Back at home I plotted those out, using the XY coordinate info in Photoshop Elements. You could use just about any program for that.
A key check is to cross back and forth across the reef now and then to create "closed loops" or paths. Then you can compare the endpoint when you plot out one set of segments with where you end up going the other path. Just using kick counts I was usually within 5% on final accuracy.
You can calibrate your kick cycles one time with a known distance rope to get the proper distance scale.
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I would make the map, put it in a ziplock bag or laminate it, then go do a dive and check it's accuracy and add in some more features.
Gradually you build up a pretty good map, both on paper and in your mind.