You must also create a Back Office Import Profile for the File Format, which will prompt you to provide information that is not present in the File Format. This is because the Submissions Client needs information which may not exist in your File Format, such as Service User number, before it is able to import a file.
When manually importing a payment file in the Submissions Client (using the File -> Import option), the 'Import Profile' list displays all the 'Back Office' profiles that exist in the Administrator. You should select the appropriate profile from the list.