Once a FTP repository has been created for the purpose of importing CSV files, you will need to create a subfolder for each list. 

A CSV file will be imported into a List whose ID matches the folder name.

You can create these subfolders:

Please note that there is one set of FTP credentials (hostname, username, and password) for a specific MailUp account.

Please note that the List ID to be used as the folder name is the list number (e.g. 1, 2, 3...), not the List GUID