Logo, favicon and custom menus are set and added. Upload your logo, retina logo and custom logo for scroll if you need one (useful if you have transparent menu and need logos in different colors). You need to also upload a double sized logo for retina displays (be sure it is named like this TreeBeardfirstname.lastname@example.org with the @2x at the end).
Header height, menu and logo position are set here so you can perfectly place them (if you have a large logo you will have to change those settings).
Responsive Mode can be disabled if you uncheck it.
Icon link for portfolio - this is the link on single portfolio pages where next and previous project links are placed (link to your main portfolio in most cases).
Default Footer and Header - these are the defaults templates for header and footer. Please note that you can set different footer and header templates for each page, but these are the defaults that will be used in case nothing is chosen at the page.