Firstly, I'm in no means an expert. I've been making my own movies on the 5d2 (topside) for about a year and now shoot film underwater. This is what I know.
The advantages of moving your camera over to full manual, as you mention is to have full control over the camera with regard to ISO, shutter speed and aperture.
Why would you want full manual control, well to create the right look you're trying to achieve on a given scene.
As you probably know though stills - Apature will give you narrow or deep depth of field.
ISO, if you aren't aware, the native ISO levels for the 5D2 and 7D are 160, 320, 640, 1250 & 2500. These are your cleanest ISOs, everything else in camera is just exposure comensated so it's in your interest to keep the values on these settings.
Shutter Speed - this effects the over all 'look' of you film and should not be confused with frame rate. Think of a large wooden wheel on a stand in front of your, rotating. Put a line on the edge of the wheel and spin it at a constant speed. Every time that line moves past the a given point is the frame rate. Say it's passing that given point 25 times every second that's 25fps.
Now, cut a 180degree wedge out the centre of the wheel (leaving the rim). Now for when you spin that wheel you will see light everytime that half passes you. This is the effect of setting your shutter speed to 1/50th of a second. Cut a quarter out and you're down to 1/100th s. You can imagine what the effect would look like when you put a moving image the other side of the wheel. The faster you get, the more pin sharp the imagery, but the more clinical and crisp the result will be.
Slowing your shutter speed will in effect make a more slurred dreamy look.
24fps is favoured by big film makers. 25fps is PAL and 30fps is NTSC (they're rounded up, but you get the point.)
The reason for flickering on land is that in the UK for example, the electric system runs at 50hz, so recording at anything other than 25fps everyx amount of frames, the footage will capture the light being off. You can see an example of this
.
(You clap 25 times a minute, I clap 30 times a minute, every now and then, we'll clap at the same time.)
This, is of course redundant underwater, but must be kept in mind if you are including topside footage in your timeline.
So these are the reasons why we would want to keep manual control over the camera.
Aperture Priority will evaluate the light levels, and adjust the shutter accordingly.
Shutter Priority will evaluate the light levels, and adjust the aperture accordingly.
Auto WB will evaluate the light levels, and adjust the ISO accordingly.
Either of these you lose control over the one element that the camera will adjust. I know the 5d2 used to (I don't know if any later firmware fix this issue.) flicker when the Aperture is being altered in the camera.
I *think* any computational changes in the camera when it's recording interrupts the recording stream.
The least problematic I've found is Auto ISO (but I've had an example of the camera stuttering on one dive when I had Auto ISO on, I've since only shot manual ISO, usually 640, but need to go back and do more tests to see if it was the Auto ISO.)
I tend to keep my framerate at 24fps, I try keep my shutter speed constant. My ISO only changes from topside to underwater. And I change the aperture manually.
I shoot Wide Angle though and my priority is to keep the aperture as closed as possible to attain the large depth of field I need.
For Macro, you will need to open up the aperture as wide as possible for that narrow depth of field.
On the 5d2 you can see the 3 colour histograms to give you an idea of the light levels and colour balance. I use this for exposure.
One other aspect you may want to look at is the Picture Styles. This is just going to be down to trial and error, but the general (topside) given is that you need to crank down the contrast and saturation to give you more headroom in your NLE for colour grading.
Setting your camera on Auto just lets the camera go off and do what it wants given the available light. Look at taking a wide angle shot of a turtle swimming past you, as soon as he gets high enough the sun's going to come into frame, the camera sees the increase of in frame light and stops down the shutter or aperture or ISO, or all three, darkening the subject out too much and in the process (possibly) stuttering the footage.
In the case, you really stop being the camera operator and are just the bloke who's carrying the camera around.
As I said, I'm nowhere near an expert and am learning as I'm going along. But I hope this helps.
