After the jPC boots, it will start the display manager, greetd, then start the labwc Wayland compositor. The Wayland compositor then runs the first, by lexical order, an executable program found in the $HOME/autorun directory. By default, it runs a Bash script configured to display the jPC administration program.
To run your own program, simply modify the Bash script in $HOME/autorun, or replace the script with your own program. Be sure to use chmod +x {executable_file} to make the file executable.