The file scanning doesn't distinguish between movies and series. From the title (and the year if included in the title) it determines what's the best match, which can be a movie or a series. If there are several matches, it chooses the most popular one.
By default it uses the name of the file and if there's no match at all then it uses the name of the containing folder. You have the option to change this behaviour using the menu "Tools->Settings" and on "Page 2" checking "File Scanning->Recognize folder name instead of file name".
How should you organize your series episodes? What I recommend is to have your files named as:
"Series Name (Year) S01E01 - Episode Name"
This way the default file behaviour will work for everything, movies and series episodes.
If you decide to do something weirder, for example if your series episodes don't start with the name of the series (the name of the series is only found in the containing folder), then it'll be more complicated. Possible but more complicated. You'd need to have your movies and your series in separate folders, set the file behaviour when you scan your movies and set the folder behaviour when you scan your series.
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