Create a link or copy the app’s desktop file to the ~/.config/autostart
to start it at qube’s boot e.g.:
mkdir -p ~/.config/autostart/
ln -s /usr/share/applications/qubes-run-terminal.desktop ~/.config/autostart/qubes-run-terminal.desktop
How to install software | Qubes OS
For opening app window in a specific workspace you can use devilspie2 in dom0: