Hello Alcina
Although not a canon user, but newish to digital, I've used my Nikon 60mm with 2x TC which brings me near enough to your canon 100mm as your playing with bigger crop factor.
I agree along with mike, I only tend to use my setup with around F16 F22, to try and gain the best DOF i can using FLASH to expose the entire image.
When i'm shooting fish i try and fill the frame and focus on the critical area of the EYES.
Example.
Click to view attachmentshot using the above combo , you will see that even though this is smaller reef fish that his pec fins are way out of the DOF, focus is on the eyes.
I try also to not shoot too many fish using this combo, and go for shapes a flat textures where i know i'll get max focus from front to back
see example, I like the sponge image in these shots as it looks like some kinda ALIEN FACE,
the whip coral reminded me of a SeaHorse
And the clam shot was just a perfect bathroom wall shot.
Click to view attachment Click to view attachmentSorry reached limit see under for clam shot
best of luck
craig