It's probably one of the first things you may want to do when you start customizing the theme to align its looks to your brand. To upload your logo, navigate to Shopkeeper > Customize > Header > Logo.
Can I upload an alternative logo for the sticky header?
Yes you can do that, you can find this option in the same page. The secondary logo you're uploading will be served on the sticky header (if enabled) as well as mobile devices.
Can I upload an alternative logo for the transparent header?
Sure, you can actually set up two different color schemes for the header elements and assign an alternative logo to each one. This give you more flexibility if you're using different header settings in different pages. There's a separate tutorial on setting up a transparent header.