From the Header section in the Theme Editor, there are 3 values that allow you to fine-tune the spacing around your logo, navigation, and the page content that appears below the navigation bar.
Logo Top Padding
This is the area above your logo. If you find that your logo is small and not naturally inline with your menu, you can add some padding above the logo to nudge it's position a bit lower.
Navigation Top Padding
If your logo is fairly tall, you may want to push down your menu a bit to be centered with the logo.
Content Area Top Padding
The content area refers to the entire section below the main navigation bar. If your navigation bar becomes quite tall (either from a large logo or several links), then it might start to cover your main content. You can use this setting to push your content further down to page so that it's not obstructed by a large navigation bar.