In shallow water in particular, when you get a significantly longer period of bottom time, I like to drop straight to the deck and then "aspetto" the reef, lying either completely still or slowly creeping across the structure with one hand while remaining as flush as possible with the bottom.
One of my favorite techniques for wary fish is to conceal behind a blind piece of structure after they've spotted you, like a rise or corner, and then toss a handful of sand or debris up above or next to you, into their line of sight. After doing this once or twice, lots of fish will actually come investigate what you're getting into. The ones that don't come closer at least tend to relax a little, thinking you're just going about your business, and will present a decent shot when you creep back into view.