The internal Reference number on a Payable is supposed to be a sequential number, like an invoice number. Any user entered references should go in the Vendor Reference field.
PERFECT FIT initially used a single field (Internal Ref), and allowed users to enter it. Over the years we have learned the value of using a sequential number, and later added the second field for the user to enter. Some time in the future Internal Ref will be locked down.
There is no real need to put the vendor code in either field, as the transactions are linked already to the vendor. And because Vend ref field defaults to being selected, you can just type over the default and enter the vendor ref field once. Leave the internal number as it defaults to a sequence number.