1: Choose Window>Workspace>Video (or Window>Workspace>Motion for CS5 and above)
2: Go to File > New, In preset choose ‘Film and Video’ and choose the size you require, eg. HDV ETC.
3: Go to Layer> Video Layer> New Video Layer From File and choose your video file. From here, all photoshop filters etc are availbale for you to use on your video. Note that working with video in photoshop can be a memory hog.
4. If you want to rotoscope or animate on top of your video, choose Layer> Video Layer> New Blank Video Layer.
You can draw on your video on this new layer, on a frame by frame basis. You can move forward and back between frames using the controls in the animation window that will be opened when you choose your Workspace> Video preset.
5. When done, export this as a png sequence with an alpha channel for transparency.