Thanks everyone! I found @mitu's answer the most useful, but thanks for the suggestions!

Ok I did that command and I got used 5.4GB(10%) with 51GB available. So I guess I just misread the File Manager.

What prompted me to misread the File Manager I suppose would be when I was scraping games and got a disk full or something else(forget what now) error message. However, I SSH'd into the Pi during the Scrape operation and perhaps that caused that error message and made me paranoid.

@Dominus yes. Google things like "retropie doom" and it tells you about replacing the wad file. Googling the others will tell you how to do it for quake and duke nukem 3d and wolfenstenstein 3d/spear of destiny. Plus tons of other doom engine/mods are explained how to do in the doom wiki