King Tut: Basic Composite for Animation in After Effects

There's a lot to compositing, but here are some of the barebones basics to get you going.
Although Nuke is more commonly used for this task, most students have access to After Effects, so I'll use it for this demonstration.

First thing you'll do is import your render layers as footage.
File - Import - File...

Select the first frame in an image sequence and make sure that the (filename) Sequence and Force Alphabetical Order buttons at the bottom of the window are checked. Click Open.

Your successfully imported footage will appear in the Project pane. If the name is incorrect, go ahead and right click, rename the selected layer. With the layer selected, we can already see a problem. After Effects is assuming this footage is 30fps when we're really wanting it to be 24fps.

With the footage selected, right click.
Interpret Footage - Main...

The frame rate is, by default, set to 30...change it to 24 and click OK.

Import the rest of your layers and make sure everything is named correctly and is operating at the correct frame rate.

We're going to assemble these pieces to the puzzle in something called a Composition.
To make a new one click Composition - New Composition...

Name it appropriately and set the duration to match to duration of your footage.

Our bottom layer in our comp will be our Diffuse layer.
Just click and drag any layer you need from the Project pane to the Composition.

Over top of our Diffuse, we'll throw our Occlude.
Next to the name of our footage, notice the dropdown menu under Mode.
These options will tell our Occlude layer how to filter through to the Diffuse layer.

We'll click the Mode dropdown and change the option to Multiply.

So here's my spaceship as a Diffuse Layer.

Here's the ship with Occlusion multiplied over it. I can do anything I want on a layer by layer basis...from changing the color of my Occlusion to blurring it out. It's all about what you want out of your final image.

If you don't want so much occlusion in your overall image, open up the options for the layer and reduce the opacity.

In our Light layer, we want to manipulate our shadows and lights separately.
After dragging your Light layer into the composition, copy and paste it so we have two.
We'll have each layer using a separate Mode in order to allow us to just control each aspect individually.

For the shadow portion of the Light layer, we'll set it's Mode to Multiply.

This instantly drops in a dark, deep shadow. If it's too much you can always adjust the opacity on this layer to lighten them up.

Separating the light portion of the Light layer is open to interpretation.
Many blend Modes will work here including Add, Lighten, Screen, Soft Light, and many others. Use whatever works best with your scene.

As always, don't forget to tweak the opacity of each layer. Most won't work straight out of the box.

Once our scene is fully composited, we might want to adjust the overall color or histogram of things. We can use any of the effects in the Effects pane we desire on each individual layer of footage, but it might take a ton of jumping between layers to get the image perfect and sometimes it's nice to have everything in one place rather than constantly spinning plates.
With your composition tab selected click on Layer - New - Adjustment Layer.

Our Adjustment Layer will show up at the top of our composition as a layer of oddly colored footage.
Any effects we place on it will apply to everything beneath it...for example I've used a Color Balance on this adjustment layer and it is affecting all my footage.

At this point use as many image control effects as you like, my favorites are CC Tone, Color Balance, and Levels but feel free to experiment with new things!