Well, with the Canon, if I am not wrong, you can onlu shoot TTL in automatic modes, not in manual. So, if you shoot Av,TV or P modes, you can use S-TTL.
To use S-TTL you need to set the mode to S-TTL (or S-TTL Low por macro), set the ACS to on (lower right button out) and set the power to 12 o'clock (upper right dial). Then, you will be able to fine tune the strobe power with the power dial (less power to the left, more power to the right).
In manual camera mode (or to shoot manual in any other mode) you should set the mode dial to M or FULL, and then set the power with the power dial (from 9 o'clock, minimum power). In this mode, the ACS should be off (lower right button pushed).
In manual camera mode you can try a kind of automatic strobe power using the Auto mode in the strobes. In that mode, you should set the mode dial to Auto (obviously) and set the aperture you are using in the camera with the power dial (ISO 100). The strobe senses the reflected light and adjusts power.
BTW, I have just remembered there's good info in this Reef Photo article.
Hope it helps.