I think I found most of the javascript and HTML related topics and I could comprehend 30 percent of them.
There's a large load of customization questions incoming, but let's start with this!

1. The Command Bar is too wide (obviously).
   - I couldn't figure anything to change that. I want it at the width of divOutput or smaller

2. The Command Bar's position is off.
   -It is partially cut off the screen at the bottom. I want the Command Bar to be a bit higher.

Edit: Fixed the image link

1. After many pointless attempts, I figured a working script to change the command bar:

JS.setCss ("input#txtCommand", "width: 955px;")

2. Its vertical position was somewhere fixed along the way and I don't know when or why that solved itself.