Setting up a Drupal 8 site for a multi-site environment with a common configuration isn't too hard, it just requires a little bit of forethought and some planning to get things right. You need to have a default configuration in mind, and then think about how each site can override this configuration in different ways. I have seen it done wrong a few times recently and once you go down the wrong path, getting things back in line again can be a difficult.
The default configuration covers things like content types, vocabularies, fields, views, enabled modules, or anything else that would make up the structure of the site. Each sub-site would override this by adding configuration for theme components, custom block placement, or anything else that is custom to that site.