user4323: I have a square adjustment layer which I have to animate to follow a screen around during a video. I want to apply some Color Correction filters to only that square, and a separate set of photo filters to the rest of the video. This way the filters do not overlap.
I tried to make the negative of that layer by duplicating and using "Invert Selection" but that didn't seem to invert the selection. I also do not know how to link the animation on the two layers (position, size, rotation, etc.)

user2197: The easiest way is to use Track Mattes. This will let you use one layer to automatically 'mask' another layer without the need for manual masking. 
Take your square adjustment layer and make any effect changes you want, then create a new adjustment layer (make sure its comp size to fit fully over the video). Place this new layer (background adjustment layer) below your screen adjustment layer. 
Select the background adjustment layer and set the Track Matte to Alpha Inverted. This action will turn automatically turn off the visibility of the top layer which is normally the desired effect, but in this case we want to turn it back on. You should end up with a layer panel looking something like this:

What this has done is the background adjustment layer is using the screen adjustment layer as a window. So wherever the screen layer is, the background layer wont be visible. 

4323: <p>I have a square adjustment layer which I have to animate to follow a screen around during a video. I want to apply some Color Correction filters to only that square, and a <strong>separate</strong> set of photo filters to the rest of the video. This way the filters do not overlap.</p>

<p>I tried to make the negative of that layer by duplicating and using "Invert Selection" but that didn't seem to invert the selection. I also do not know how to link the animation on the two layers (position, size, rotation, etc.)</p>
 2197: <p>The easiest way is to use <strong><a href="http://helpx.adobe.com/after-effects/using/alpha-channels-masks-mattes.html" rel="nofollow noreferrer">Track Mattes</a></strong>. This will let you use one layer to automatically 'mask' another layer without the need for manual masking. </p>

<p>Take your <code>square adjustment layer</code> and make any effect changes you want, then create a new adjustment layer (make sure its comp size to fit fully over the video). Place this new layer (<code>background adjustment layer</code>) below your <code>screen adjustment layer</code>. </p>

<p>Select the background adjustment layer and set the <strong>Track Matte to <code>Alpha Inverted</code></strong>. This action will turn automatically turn off the visibility of the top layer which is normally the desired effect, but in this case we want to turn it back on. You should end up with a layer panel looking something like this:</p>

<p><img src="https://i.stack.imgur.com/myS3i.png" alt="Sample Layer Order"></p>

<p>What this has done is the background adjustment layer is using the screen adjustment layer as a window. So wherever the screen layer is, the background layer wont be visible. </p>
