Here's what I did, being new to U/W photography - from the Backscatter website - there's a guy there that writes excellent articles for beginners. I realize that this technique may not be of much use to many on this site that are really into this stuff in a semi-pro or pro level, but it worked really great for me:
When you get in the water, don't go very deep without setting the focus, so you still have good light and contrast. Set it by putting it on AutoFocus, zoom to full wide, and then focus on something stable about 2 feet or 18 " away. Then use the focus "Lock" function to lock it. From then on just about anything non-macro that you shoot will be in focus (assuming a standard type of lens) and there won't be any hunting done by the camera. Letting the camera do the initial autofocus means it will be sharp because it can do it much better than you can using the LCD. The when you lock it you have focus set for the stuff you shoot thereafter. I did that on my very first trip and all of my footage was good from a focus standpoint (other things were, well, in need of practice but overall I was pretty pleased).
I also did a practice session in a swimming pool where I got used to the MWB process with my camera (I have the SR1 but I think the menus and focus stuff and etc. are very similar) and it really helped. I made a small checkilist of initial settings and went through that each time before I mounted the camera in the housing. I started the list using the settings the housing manufacturer recommended and then made a few modifications to suit personal preferences. As I say, all of the foootage was good and usable - I have to practice on movement, framing, and etc.