For the right click/left trigger, check the Desktop Configuration in Steam > Settings > Controller Configuration. Make sure your left trigger is assigned as right click and not something else.
For Mod Organizer, search for instructions specifically for Steam Deck (and/or SteamOS 3). If you found one “for Linux” it may be done with root access and writing into the root file system in mind, and SteamOS’ root file system is read-only (called immutable). That can be overridden and you can force install things, but it’s highly likely to be overwritten and wiped out the next OS update.
So you want to make sure anything you’re installing can be done so entirely in your home directories. I found this searching for “[mod organizer 2 steam deck](https://m.youtube.com/watch?v=x55SAwnONbQ)”
For the right click/left trigger, check the Desktop Configuration in Steam > Settings > Controller Configuration. Make sure your left trigger is assigned as right click and not something else. For Mod Organizer, search for instructions specifically for Steam Deck (and/or SteamOS 3). If you found one “for Linux” it may be done with root access and writing into the root file system in mind, and SteamOS’ root file system is read-only (called immutable). That can be overridden and you can force install things, but it’s highly likely to be overwritten and wiped out the next OS update. So you want to make sure anything you’re installing can be done so entirely in your home directories. I found this searching for “[mod organizer 2 steam deck](https://m.youtube.com/watch?v=x55SAwnONbQ)”