[shinner]

Your anime names are originally absolute numbering right? eg. Naruto 305, not S15E02 or something? If so, try to use regex, it's much less trouble.
Now, create an advancedsettings.xml file, and add this in:

Code:

<advancedsettings>
    <tvshowmatching action = "prepend">
        <regexp>Anime[\\/].*[/\._ \-]()([0-9]+)(-[0-9]+)?</regexp>
     </tvshowmatching>
</advancedsettings>

Edit the "Anime" in the code above to the name of your source folder. This regex should handle multi-episode files.

Thanks to gates' post.