The Site basics section at the top of the Loupely Canvas settings screen gathers 3 site wide things in one place: your logo, your favicon, and your menus. It is there for the parts of a site that are tedious to hand code and that WordPress already stores well. If you would rather code all of it yourself, you can skip the section entirely; nothing here is required.
Finding it
Go to Appearance, Loupely Canvas. Site basics is the first section, with its own link in the jump nav at the top of the screen. For the logo and the favicon it shows the current state and a button straight to the right control. WordPress stores both, so they stay in sync whether you set them here or in the Customizer.
Logo
Set a logo image from the Site basics panel or under Appearance, Customize, Site Identity. Once it is set, place it wherever you want in your header or footer with the {logo} token, which renders a linked image with the class custom-logo for you to size with CSS. The placing is covered in using tokens in the header and footer.
Favicon
The favicon is the small icon a browser shows in the tab and in bookmarks. Set one under Site Identity and WordPress prints the icon tags into every page on its own. There is no token and no code for this one; setting the image is the whole job.
Menus
Build a menu under Appearance, Menus and assign it to the Header or Footer location that Canvas registers. Then place it with {menu:header} or {menu:footer}, or call any menu by its slug with {menu:a-menu-slug}. A menu renders as a plain list with the class lc-menu, yours to style. If you keep your navigation hand coded in your header markup instead, that works too; the menu locations are there for when you would rather manage links in the WordPress menu screen.
None of this changes the passthrough model. Your header and footer are still the raw HTML you write. Site basics just hands you the logo, favicon, and menus to drop into that HTML when coding them by hand is not worth it.
