Because I'm running a server, I moved my Pi's file directory to a USB device using this tutorial, which means that I'm booting from an SD card, but all of the stuff I need is in a USB drive. How can I back up both my SD card and my USB so that I can save all of my settings if something crashes. Better yet, is there a way to backup my files via FTP or SSH?
Your server most likely runs headless, remote access is via
USB drive and SD card are both known to your system via fstab. So, it actually doesn't matter what they are, physically.
If you want a simple method with a small footprint, please consider rsync.
rsync plays nice via ssh, you probably want exactly that to backup your data to another remote machine. Authentification can be realized via ssh-keys.