You just add the flatpak to steam and then you have to edit the launch arguments for the shortcut (in steam, right-click the shortcut, properties). In the properties you just add the cli arguments for launching the game you want or w/e. If you want to make multiple different games, atm I would suggest maybe trying out BoilR which can at least go through multiple files, but if it's a manageable number, you would just create the same shortcut to the flatpak for however many games and then edit each shortcut for the individual games you want.
For adding the shortcut to steam: Desktop mode => Start menu => Navigate to Yuzu => Right click menu entry => Add steam shortcut or w/e
In the future, there will probably be a plugin for it, if/when I actually get time to add the functionality and make a PR to QuickLaunch.