I always use AF-C. I don't see the point of AF-S when you have AF points all over the sensor + unless you plan to take pictures lying all over the reef (to stay still).
With the 90mm I use a mix of modes depending on the subject. When I am shooting fish I usually use Wide or Zone AF - as the camera is really good at identifying the subject fast and accurately - why make it more complex than point and shoot.
WIDE AREA (no problem picking up the edge of frame damsel, despite shooting in the sun):
ZONE - offers a bit more control - with a smaller area active (in this case moved to the left of the frame for the face):
I often leave Animal Recognition on. It does not always engage, but it is usually useful when it does. I don't have Insect on my camera (because Sony are useless at firmware updates)
WIDE with Animal Detect - picked up the cardinal fish eye easily:
For more crittery subjects - slower moving, often smaller, I will use Expand Spot or Tracking Spot. If the subject/situation means the subject is moving more I use Tracking Spot (this is analogous the 3D tracking I used on my Nikon).
EXPANDED SPOT: moved onto one of the eyes (this is shot with the Nikon 60mm, rather than the 90mm, but I would have done exactly the same with 90mm):
I tend to use the same for Super Macro - but may turn off AF With Shutter (I usually have it on). Although I have found that the camera is perfectly happy running AF with the SMC-1 and SMC-2. When we were shooting the blue belly blennies the camera would face recognise them and lock on the eye through both he SMC-1 and SMC-2 - so I even used Zone with them had the Af on the Shutter Release - just point and shoot.. I will wait for a full on macro trip before deciding exactly what I prefer and it will probably vary a bit between subjects. Nudis with Back Button, fish with obvious faces using AF on the shutter and subject recognition, with Zone.
ZONE with Subject Detect had no problem locking on this eye and holding focus:
I'll add some example images to this post when I get on my computer. Photos added now.
Alex