In manual mode, every change of either aperture or shutter is "compensation" in that it moves exposure up or down. That is why there is no need to (and no ability to) use the EV compensation button. "Compensation" only allows you to manually adjust an exposure that has been automatically calculated by the camera in one of the auto-exposure modes.
The EV comp scale is also the manual exposure scale. In manual mode, it shows you how far over or under you are from the camera's recommended exposure. It will blink a warning if the manual exposure you have set is more than two stops over or under the camera's metered exposure. Once you manually adjust the aperture or shutter to bring the exposure within two stops, the blinking will stop. When your manual exposure hits the middle mark, your exposure is consistent with what the camera recommends (and with what the camera would automatically set if it were in an auto mode).
If I an NOT using flash, I prefer to use the camera in an auto exposure mode and use the EV compensation to fine-tune the exposure up or down to get the effect I want. This is much faster than trying to set manual exposure, which you must change with every shift in the light, and every shift in composition. Better to let the camera handle the large scale adjustments automatically and you just fine tune. Much faster too. Most pros I know in the nature field actually work like this (almost all of them use the aperture priority auto mode).
If I AM using flash underwater, I usually manually expose the scene for about - 2 stops. Choose the combination of aperture and shutter that gives you what you want (smaller aperture for depth of field or faster shutter --but no faster that 1/180 which is the max flash sync speed -- to freeze motion. I then use "TTL" flash to auto-expose the main subject that is lit by the flash. This usually gives dark, deep colored backgrounds through the manual settings, and a bright, vibrant subject that is lit by the flash.
That is only a suggested starting point. Since you seem to be learning, it is a good place to begin and see if you like the results. You seem to want to move beyond "auto everything" and that is a a good thing. You do have to pay more attention because, as I said, if the light changes or you point your camera in a different direction for a new shot, you do have to check the manual exposure to see if you need adjusting.
