Hello DCINV, 

Welcome to the Community page, 

So for the first part that is not something we can help you with, if the import data is coming from a 3rd party, its up to their software to prepare the data to send to us, if they don't prepare something to work in the payment method field, its not our responsibility at quickbooks to fill it in, its technically not a mandatory part either, so if its missing, it wont affect the transaction, so you might want to look into that more. 

as for the second part of your question, it sounds like you want to turn off the Go Cardless direct debit payments option for a particular customer? If that is the case, that isn't possible to do so without removing the mandate from the customer itself, it'll always try to take it via Go Cardless so long as the Direct Debit mandate is established.