Difference between theming app and themes
The theming app is the recommended way to change the look and feel of your Nextcloud setup. That app is continously updated when elements in the Web User Interface change and keeps existing setups compatible. The theming app not only changes the Web User Interface, but also the color and logos in the emails that are sent out (i.e. share information, activities, welcome emails, ...). To configure it, just go to the admin settings and choose the "Theming" section on the left. If it is not available, make sure that the app "Theming" is enabled in the app management section.
In the future more and more of those settings will also be used by our sync clients on iOS, Android, macOS as well as Windows.
Since all theme-related modifications are performed in the admin settings panel, this significantly reduces the maintenance efforts needed on your side, during upgrades per example.