If you have access to a Windows machine, that is the easiest method.
Setup everything as you want it, with Mod Organizer 2 (portable), on the Windows machine. Then use the Linux installer of MO2 on your Steam Deck. Overwrite the contents on your Deck with the directories from your Windows machine. You may need to mess with the path arguments in Steam to open MO2 when running Fallout.
I’ve heard you can mod directly from the Deck, but it’s more tedious. I haven’t done it this way, so I have no advice.
What's the easiest way to transfer files from windows to the deck? This seems like it should have been easy but I remember spending several frustrating hours setting up ssh only to have it frequently fail for reasons unknown, last time I tried this around when I first got my deck. Does a USB cable work if you plug it in directly? I don't have a USB3>C data cable but I can probably get one.
I don't know if this is the easiest way, but it has worked well for me. I have a folder on my computer set up to be accessible from the local network. When I need to put some files on the deck, I switch it into desktop mode where I have a shortcut to the network folder. Then I just take the files out and put them wherever I need them on the deck.
Unfortunately as the deck is a pc you cannot copy files between them with an usb cable :/. but you can share a file with samba on your windows machine and open it with dolphin on the deck ;)