Last update, this issue is closed.
It seems that there is an issue when I was trying to use the terminal built into the ajenti panel. I was using ajenti to try and make my life easier when I am not at home, but that turned out to be a bad idea. Anyway, everything works just fine when I ssh into my server using bitvise.
As far as uploading the library, everything in the /public directory is exposed on the website root. So, you can generally put the library anywhere in there.
This is what I was looking for! Thanks!
As for loading a js file at the end right before the closing body, which file should I place the script tag?