Colors and CSS for any website are established through a "Theme" or a "Local Design". These can be edited by Admins via the interfaces described in the Theme Editing: Color Picker and CSS Inputs page.
Themes are color schemes and CSS that can serve multiple sites and be easily alternated within any site. Changes to the colors or CSS of a Theme will impact all sites using that theme. For this reason the default setting is not to allow the editing of Themes by Community Admins.
A "Local Design" serves a single site and cannot be made to serve a different website or other sites without manual replication (copying colors and pasting CSS into another site or a Theme). Changes to the colors or CSS of a local design will impact only the singe site using that Local Design. The local design option is created specifically to allow a Community Admin to have full control over his/her website's colors and CSS without those changes impacting other websites.
Choosing a Theme or Local Design
The toggle between using a Theme or a local design is on the Theme tab of the Site Setup area. If "Local Design" is selected there Color Picker and the CSS editor are also presented to the user on the Theme tab. If "Theme" is selected the user is presented with a list of available themes from which to select.
Local Design is generally the best option only for Community Microsites where a Community Admin wants total control over a site's design.
For more information see the Theme Tab page.