Thanks for your relies David and Drew. I am sorry, I wasn't very clear. Let me try to rephrase, as I think my terminology and general explanation was a bit confusing.
I understand the camera doesn't have Auto Focus while shooting. I was referring to focusing before the shot.
I also use Quick Mode in Live View, I try to focus on the reef, a few feet away, before I hit the record button. I do this by hitting the 'AF-ON' button, until it focuses, then hit the record button.
The 5d mark ii has 9 focus points on the screen. Which currently I have the camera set for multi point focusing. Typically, it will light up several of these focus points, when I hit the AF-ON button.
Also, on the camera it allows you to choose your focus points. By hitting the 'AF Point Selection/Magnify' button on the upper right hand side of the back of the camera. It can be set to have all focus points available to focus or just one of them. Letting you choose which one, you want. My question is. Do others have all 9 enabled for video, or just the center focus point enabled?
The reason I ask this question, is I was poking around other non underwater websites, and people claim that the outer focus points are not good, and to do a center focus point only. I was wondering if the reason some of my footage was out of focus, was because I had all 9 points enabled. As the camera would use multiple focus points, instead of just the center.