How do I organize my library?

Make sure the directories immediately below your library path are named exactly to the series' title. This will make it easier to match the title on mangaupdates.

Anything resembling the following is valid.

Library path
|--- A Title
|    |--- file_01.zip
|    |--- file_02_01.zip
|    |--- file_02_2.zip
|--- B Title
|    |--- file_01_1.zip
|----+ Subfolder #1
|    |--- file_1_2.zip
|    + Subfolder #2
     |--- file_1_03.zip