There could be a new Encyclopaedia to write about this subject, and don't forget that DB is a world forum: different fish, different bottoms, different hunting cultures....
But since a "reef basics" thread is started, let's see how to fill it with a common effort.
Chapter 1: directions and approach.
Check current and sunlight: they can make the difference (best is, when possible, to have both current and sunligh from your back). Look for places where you see any kind of structure that may "call" the fish: an isolated rock, a "step" in the terrain, a steeple rising up from deep to shallow, a boulder different than the others, schools of bait moving around, a bush of weed in the middle of uncovered terrain, heaps of boulders collapsing to deep, a shelter from the surf, the estuary of a stream, wrecks or dumped junk of any kind, in three words, anything looking special.
Duckdive....(please fill in)