If you did not "Set Content" when you added a source, you can do so later by selecting the source and bringing up the contextual menu ( You can also "set content" for subfolders, even if the parent folder has content set that is using a different setting.
For example, you can have a folder for your TV shows, and in that folder have a folder for "Star Trek" that contains the different Star Trek TV shows.
If you do this normally then Kodi will think that "Star Trek" is one single show, but if you set content on that specific folder, then it will scan everything in correctly.
Avoid adding a subfolder as a separate source, as Kodi will might make duplicates if there are two sources that lead to the same files.
Our recommendation: choose the least complicated option that does what you want.