By default R2 is left click and L2 is right click but I prefer the opposite. I was able to change this with the following:
Settings > Bluetooth & devices > Mouse > Additional mouse settings > Switch primary and secondary buttons (default is disabled and I set it to enabled).
I also confirmed that it worked with Steam Deck Tools's SteamController shortcuts and does not swap L2 and R2 when in game.
Interesting preference! I think for dual-boot purposes, it's best to stay with the default settings that mirror SteamOS configuration, so I will not include this in the guide.
Just another suggestion that was helpful for me.
By default R2 is left click and L2 is right click but I prefer the opposite. I was able to change this with the following:
Settings > Bluetooth & devices > Mouse > Additional mouse settings > Switch primary and secondary buttons (default is disabled and I set it to enabled).
I also confirmed that it worked with Steam Deck Tools's SteamController shortcuts and does not swap L2 and R2 when in game.