These options can be found by navigating to Shopkeeper > Customize > Header Layout & Style > Header Layout & Style:
Why I can't see my menu if I select a centered logo layout?
Once you decided to use one of the two layouts with a centered logo and a part of the menu on left and one on the right, you need to know that those require to build two new menus. One which will appear on the left and one will appear on the right. After you created these two, make sure you choose for each one the options marked with red: