I have now animated my animatic. After setting everything up in After Effects using PSDs of my scans, I opened particular pieces in Photoshop and edited elements on to multiple layers, then right clicked the files in After Effect and chose 'Replace with Layered Comp' which switched out the regular file for a composition. I them opened up this composition and then added keyframes to various properties such as position. This allowed me to move layers over background layers.
Here is a preview:
