You can do an "apply" check, for a zero amount, pick up all the negative numbers (payments and credits), then apply all the positive numbers (invoices). - Just as you did in Plus.

One way to avoid this is to assign the invoice number to the prepayment when it is created.
You can use the date in the form of yyyymmdd as an invoice number for unknowns.
You have reference and description fields available in Invoice entry which can be used for the Vendor's invoice number if you use your own assigned one when you receive the final invoice.

You will have to decide which method works better for you.