I've been trying to troubleshoot the same thing. The farthest I got was to add a SaveImages step in my CP pipeline, which then writes the aligned images to my filesystem. I then tried to incorporate those pathnames into my properties file but couldn't get CPA to load those images. I'm not sure I got that bit right, though.
Confusingly, the ExportToDatabase step in CP has a box where you can select which images to make thumbnails out of...but this either doesn't work as intended or does something different that what I'm expecting. I have my aligned images selected in this step, but it's the raw images that get shown in CPA.
If you or someone else gets this working I'd love to hear about.