Yes, Cassius, we use the actual AE project as a source of animation (it is 2 dimentional games, “moving pictures”). And we do exactly as you have said. Batch exporting from photoshop via “Export layers to files” and then import it to AE. Actually here our problems started. I have two options:
1)put PSD file as a background layer, then drop my PNGs to the same comp, and start my tedious work placing it to the proper positions
2)import PSD file as composition with the layers trimmed, and then start my tedious work replacing the layers with the PNGs one by one.
As for me, the second way more preferable, it strictly keeps the layers position and just faster to proceed.