How can I file an automatic debit order for fees payable in the international phase?

You can do this via Central Fee Payment under Automatic debiting management or via EPO Online Filing, Online Filing 2.0, PCT-SAFE or ePCT, using Form PCT/RO/101, Form PCT/IPEA/401 or PCT-SFD.  A separate section in these tools allows you to select automatic debiting as your means of payment.