Thanks, I did find that thread but it does not have the solution for me.

You can just visit the Vendor --> Payments Menu are create a Payment there, referencing the PO, then when you DO get the Bill, you can apply the prepayment and the Bill (when it arrives) will then show the remaining open balance.

This does work when manually adding a payment. But when I create a bill and then want to register a payment,  i cannot link this to the purchase order?