How can I modify this area and style it a little bit? I am making a new theme and I think that modifying this area will make my theme look a little nicer.
Edit your navigation templates.
Would you happen to have that .zip file? It is no longer working.
AdminCP/Templates & Styles/You theme/Templates/Navigation Templates.
And CSS!
AdminCP/Templates & Styles/You theme/global.css and modify all classes navigation.