Everything begins with the header.php file which starts at line 29 <header id="cel-header"…..
…down to line 117.
Container css is in the style.css around lines:
184 for the #cel-header
210 for the #social-wrapper
2228 for the .main-navigation (menu container)
You will see classes like "container" "row" and "span4…etc". These are Bootstrap framework related, so I recommend not editing these which are found in further below in the stylesheet.
I just looked at your screenshot….the menu location is not difficult as there is a theme option setting for margin position in the Nav tab of the customizer. The logo placement should be a little easier to position than what I imagined without seeing a screenshot and would just be an absolute position with a z-index. However, you might have a challenge with the responsiveness of the theme in mobile view so you will need to explore the media queries to position it on small devices.