i would be happy to tee up a meeting and go through the options i mainly use.
i have to be honest though, i rarely take it out of auto, unless i am attempt macro or shoting fast moving subjects.
canon are a great piece of technology, and i would be very surprized if you could fault them.
however taking good-clear photos is all a numbers game and practice. no matter how good your equipment is, the photo depends on a number of variables, which includes how the diver approaches the subject. as a top underwater photographer once told me...water is your enemy! get close, then get closer! (not so easy when holding your breath)
ps- ISO is shutter speed on digital cameras, the faster the shutter the more light you need. otherwise you will get grains in your pics.
pss- hope to see some of your pics in the vic freediving photography comp.