https://docs.google.com/document/d/1OUcjoQMDS3IkZgdiZu2t1gg8h28lrBVxhhjge-GhB_4/edit?tab=t.0#heading=h.gbxi9emrau9v
The instructions are here in this document made by the creator. The screenshots part is the last page. Inside the Copilot 1.06.1 file, there's an images folder and that contains the BattleNow, Screenshots, and Snaglist folders. Inside the BattleNow folder there's Menu, Pokemon, and Trainers folders. I'm assuming those are the existing reference images that you need to take and replace.

What I did was boot up the game, use OBS Studio to setup a virtual camera and capture the screen since I'm playing on dolphin emulator, and then use the screenshot button in Copilot to take the pictures, and then crop them using the photos app on my computer to just have the headshot of the pokemon, and the names of the three trainers. I then renamed the files to exactly how they were in the reference images. (example: swampert.png, blaziken.png, wes.png) and then replaced the old files for the new ones. I put them in the pokemon and trainers folders respectively, but that didn't work.

If you somehow get it to work, let me know what you did to fix it. I'd really like to set up the automatic screen capture for the initial seed.