From what I've read, where payments are made to employees of their net pay by BACS, we will need to add a BACS reference to the payments so HMRC can identify them and see that all payments are made.
However HMRC have a talk and in it they categorically stated (and couldn't have made it any clearer) that the net payments to employees were of no interest to them, the code only needs attaching to the PAYE payment. This was queried by several people in the room who had the same original idea as me and she again said "No, ONLY PAYE payments".
I can find nothing anywhere that says this, but plenty saying you need to attach it to net wage payments made.
Can anyone shed any light? Does HMRC not understand their own systems (and this was an RTI specialist...)?