The height that your logo should display at. It's recommended to upload your logo at twice the size you set this at in order to ensure crisp rendering on higher resolution displays.
If you are trying to have your header navigation completely see through before scrolling, setting this very low is not how to achieve it. The fully transparent style as shown on many of the demos is the option titled Use Transparent Header When Applicable which is available in the Header Navigation ~ Transparent Header Effect tab.