Hypertext access, or .htaccess files, allow you to change the Apache configuration on a by directory basis. However, you should always use the main server configuration file to do configuration changes whenever possible. This is because when Apache is configured to process .htaccess files it looks at every directory underneath the current directory to see if there are any files present, resulting in a slightly longer page load time. Although this might not be noticeable with low traffic levels, at high traffic levels it can cause sites to slow down.
I recently wrote a post about setting up a multi-site configuration setup using the Configuration Split module. That post was written after I did research into how to set up configuration splits and use them to create multi-site setups in Drupal. One thing I realised when doing that research was that although it's quite easy to get setup with that kind of setup, it's also easy to get it wrong and create a setup that really doesn't work.
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.