You can change the logo, favicon and apple touch icon the same way as for the dokuwiki template.
If you enable doLogoChangesByNamespace in the template's configuration, Writr will use the closest logo as the site logo. Namespace Logos can be added using the media library. To show a different logo in a namespace, just make sure to add the custom logo.png in the namespace. This feature is recursive.
If you enable doLogoLinkChangesByNamespace in the template's configuration, Writr will set the logo's url to the same namespace it found the logo.
If you enable doTitleChangesByNamespace in the template's configuration, Writr will set the title found in the closest nstitle.txt page.
If you enable doTaglineChangesByNamespace in the template's configuration, Writr will set the title found in the closest nstagline.txt page.