My scripts for setting up QubesOS.
Running these scripts should be very straight forward. For the default Fedora template, run fedora-gnome.sh to trim it down first.
After you are done running those scripts, any other script can be used in a different template based on those trimmed down templates to create their respective virtual machines.
If you want to install Flatpak packages, install them inside of an AppVM as a user Flatpak and enable the update-user-flatpaks.service as a user systemd service for automatic updates.
It is recommended that you follow the docs here to make a prompt for root access on non-minimal VMs. dom0.sh already takes care dom dom0 so you only need to worry about the guests.