Just got an E-620 myself, though no plans for underwater use just yet.
You have to turn your custom controls feature on. That control is the little icon which looks like two gears which are titld "Menu Display". The 5th entry in the menu heading which looks like a wrench.
Flash settings are accessed through [Menu]. Scroll down to the 4th entry, "Custom Settings", which looks like two little gears. At the bottom of the first page in that entry is the flash control. It has a little lightning bolt and a capital "F". Right arrow into that entry and you will see a +/- control. Set that to "On" so you can control the flash level. Hmm, I can't say that I see any way of adjusting anything there. Is this what's got you puzzled? The book says it's just linked to the +/- exposure setting.
Set the bottom control "Auto pop-up" to on. That way if you forget to extend your flash, and if your housing doesn't have a means to push the flash button, you could deploy the strobe by taking a picture in "Auto" mode.
Don't know how experienced you are. Check out the stickies at the beginning of the Tips and Techniques section. Alcina and Gilligan provide some very good advice there.
My advice: use manual mode. I set my aperture to ƒ8 -ƒ14. Without using my strobe I take some photos, adjusting the shutter speed to obtain the background color/hue I want. Then, with the strobe, I use its flash controls to properly expose my subject. Faster shutter speeds help reduce motion effects like waving fins or antennae. Lower ISO settings (80-100-200) are usually less grainy appearing.