Step One!

OK, step one.
Get your movie file that you want to put your 3D animation in to. Make sure it's something that can be opened in AfterEffects, so a .mov is a safe bet.
Now we're going to put that in to maya.
So open up the file you want to use for animating. Perhaps a character or object you want to put in there.
This is what I've opened: The Moom rig

Now we're going to create a camera to use for our animating.
I'm going to use default tool shelves for everything so you won't have trouble finding anything.
So go to the bar at the top and click "create>cameras>camera"

Now, while the camera is selected we can use the move tool to position it. But it's a little easier to position the camera through the view finder, so we're going to go to the lower bar and select "panels>look through selected camera"

Now we click on the attribute editor icon at the top right

Of these three icons it is the one on the left

Now we're presented with a list of options and drop down bars. The one we're looking for first is the one labeled "movement options"

You need to make sure "Undoable Movements" is selected. That way if we accidentaly move the camera later on we can take the action back and won't have to spend forever trying to position things right again.
Next we need to go to the "Environment" section

Next to "image plane" click "Create"
On this new menu, scroll down until you get to the part that says "type". Leave that as it is for now, check the box that says "use image sequence". (the image name box will be empty for you just now)

Next click on the little folder next to the "Image Name" box. Now find the movie file you want to use for compositing.

 Now your window should look a bit like this.