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You can do it all on one shape layer using Merge Paths/Intersect. Carefully study this screenshot. I'm showing you everything you need to do to make it work.
You are going to need to Group all of the shapes and paths that create the character. In the screenshot, you will see four rectangles and an ellipse creating the character. Below the Character Group, you add Merge Paths and set the mode to Add. This will treat all of the shapes as a single shape.
Just below the Character Group, you add a rectangle. I named it the Reveal Rectangle. You'll need to add an expression to the Transform: Reveal Rectangle/Anchor point that points to the half the Y value of the Reveal Rectangle/Rectangle Path 1/Size property so that you can animate the or the scale of the Reveal Rectangle 1 and have the bottom edge stay put. Here's the expression:
y = content("Reveal Rectangle").content("Rectangle Path 1").size[1] / 2;
[0, y]
Next, you add a second Merge Paths set to Intersect below the Reveal Rectangle and set the mode to Intersect. When you add Merge Paths it also adds a fill and stroke that take over all of the fills and strokes in shapes that are being merged so you can just delete all of the fills and strokes above the second merge paths. I usually do that to clean up the layer. The two fills you see in the screenshot are the only fills in the entire shape layer. There are no strokes added.
The next step is to duplicate (Ctrl/Cmnd + d) the Character Group and drag it to the bottom of the stack. All that remains is to add a fill color below the Character Group Copy and set the color.
I do this kind of thing all the time. With a little practice, you'll learn what to select when you use the Add menu so things like Trim Paths and Merge Paths show up in the right spot. If you end up with one of these animators in the wrong place you can just drag it where it needs to go.
I hope this helps. If you need to, download the screenshot for a reference. Duplicate the screenshot and you will have what you need for the animation. Here's a project file for you to look at.
The second option is to have two different colored copies of your character layer and an animated rectangle above the top copy. If you then reveal the modes column (F4 if you only have the switches column visible) you can then set the animated rectangle as a track matte for the top copy of the character. I prefer to use the first method that I showed you. I think it renders faster and the comp is simpler. Once you are familiar with all of the shape layer animators and you are comfortable with the search field in the timeline, it doesn't take much time to create this kind of animation.
I'm not seeing a merge paths option when I import my layers into after-effects from illustrator. Is this because the shapes aren't being made inside of after effects? Since it appears that I am stuck with the second option you mentioned, am I supposed to create 2 different colored animated rectangles and place it on top of these top layers? Sorry I am still a novice with after effects and this seems a bit overwhelming for a newbie like me.
Ok I think I kind of got it. The animation looks right at least when I play it back. I created 2 shape layers and then changed up the positioning using keyframes and selected track matte like you suggested. Was this what you were referring to earlier?
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