Wanted to close this off after I thought about how I wanted to organize this.

Here's what I've done.

I converted all the .bin files into .chd files to save on a little bit of space all around. In roms/psx/ I created a hidden .chd folder where I have subfolders for each game and their respective .chd or .CDX files. In roms/psx/ I have a several .m3u files, one for each game, that each point to the .chd directory, and the individual game folder where the relevant game files are located. This allows me to keep the roms/psx/ relatively clean which is what I was going for.

I really appreciate everyone's help in getting me to clean up the roms directory!

@SonPluck /dev/shm/runcommand.log

It won't work if you remove the SD to plug in another computer because files under /dev/shm are RAM based, which means that they only exist while the raspi is on.

@windale

You don't have to unzip ADFs. UAE4Arm can load ZIP, ADF, DMS, EXE, ADZ and RP9 formats in the floppy drives.

I have updated the wiki to reflect this.
https://github.com/RetroPie/RetroPie-Setup/wiki/Amiga