Use of supplier credit note

I need to pay deposit to some suppliers. Then, I create a down-payment invoice, and register the bank transfer.
When I get a delivery and final invoice, I register the invoice and I want to use the credit note to register the payment.
But the only thing I can do is to register credit note lines, which puts the full amount to 0. But the due amount remains the same!!!
According to me, it should not come into the lines of the invoice, but into the payments, as it does for crecit notes for the clients.
Does anyone have a clue?

If you have a transactions like Advance Payments or Deposit to Suppliers, You need to create a bank accounts it is called, Advanced Payments Supplier,

But First, create on your Chart of Accounts on the Current Assets side below to your Accounts Receivable

Second, You need to create a bank Account called Advanced to Supplier, as shown below

Then if make advaned payment to Supplier Do the following, as shown below

Then if you received the Items or Products, etc. … then you need to pay to Supplier using the Bank as Shown above.

Then same you need to do with the opposite side, Customers Deposit,

On this way, you will be safe from Auditors or any other means. That’s all you need to do.

I tried that scenario you made, but the end results would not be great.

Hello isoscent,
Thank you very much for your input. I am pretty sure that it works.
I use this system to run a balance account with an agent on a foreign market who handles payment for me and runs a permanent deposit, and it is quite easy.
Regarding suppliers and clients, it is a pitty that the system implemanted into the software is not fully operative.
Again, thanyou for the support.