What kind of expense are you entering? For checks the check number serves as the reference number. You can edit the check number when you print the check but it must match the number on the printed check. For transfers you cannot edit the reference number. I can't say whether you can edit them for electronic payments since those are not used in the US and are outside my experience. But my very strong guess is that they are not editable cause the church financial system would want to make sure they are unique.
Why do you need to edit the reference?