Page not centering

Using the Aegaeus theme, I’ve chosen the “Boxed-Layout” since “Stretched” doesn’t actually stretch out all the way. A couple of problems:

1. My menu and footer seem to be slightly out of the “box” of the layout and not centered. This is on every page. How can I get it to center?
2. Every other page has what seems to be an empty sidebar that’s slightly greyed-out. How can I get rid of this empty sidebar and the pages stretched out.
3. How can I get my main menu bar to center?