The fist time I tried to shoot video with the Sony a99 I got really frustrated becaused I wanted to set the shutter speed and aperture manually. I knew that to do this I would have to use manual focus, so I would turn the top dial to M (manual), set the values I wanted then pressed the record button, but every time the camera started recording it would switch back to auto mode, changing the shutter speed and aperture as I moved the camera around.
Eventually I figured out where I was going wrong, and since I think a few other people might have the same problem I had, I thought I would share how I fixed it.
Instead of setting the top dial to M, set it to the Film Mode. Now press the Fn button, this should bring up Video menu with lots of different setting options. The first one of which (the top left hand menu) is the one you want. Select it with the direction pad, once inside the menu you will then get the option to either let the camera set the shutter speed and aperture automatically, you setting the shutter speed or the aperture manually or you setting both manually. Now all you have to do is choose the one you want.