In the Logo & Favicon section of the theme options you can setup your logos for the various locations and states of the header.
Setting the logo
You can setup a different logo for normal site header, where the header has a solid background color, for the transparent header & for the Top of the sidepanel, which is visible on mobile devices.
In addition to selecting the image file for each of these states, you should set the desired width of the logo, in the 'Logo width' setting for each of this states. So if for example you want your site logo to be 200px wide, you upload an image that is at least twice the desired dimensions, (400px in this case), and set the 'Logo width' setting to 200. The aspect ratio of the images are respected (Thats why you only have to set the width).
Setting the favicon
On the bottom of the same page you can set the site's favicon (Site Icon). A 32x32, or larger png is recommended.