Help changing my boot sequence

Hey everyone! sorry to bother you all but I'm trying to change the boot sequence on my RPi3
I am currently running jarvis and the other day after watching a tv show off an old usb, I forgot to take the usb out and the next time I booted the Pi up the usb I left in managed to corrupt one of my boot files on the mSD and i had to reinstall my OS again. Was hoping someone could help me with what to change my cmdline.txt file to so that it doesnt happen again! Thanks!! Ive tried looking everywhere!!