Creating a Vat only invoice or credit can only be done manually, not through the order processing area.
A Vat only invoice is created in exactly the same way as a normal manual invoice except that there is no goods value.
This means that the nominal code entered on the line will not be used and the Vat liability will be coded according the the Vat Code on the line and the Vat Country on the header.
The line entry should look something like this. With nothing in the Goods value and the vat to invoice or credit in the Vat value.