Customer and Vendor - Deduct the payment of vendor fro received ammount

Customer and Vendor - Deduct the payment of vendor fro received ammount

Hello Everyone,

I'm around this question for more then a day, and no clue how to get it done. I have googled for everything, and the only solution that would supposelly work, it is not.

 I have customer A, which pays me 10.000 USD for an invoice of 11.000 USD, because he has deducted the ammount of 1.000 USD of an invoice he issued to me.

I have issues sales invoices, have registered vendors invoice, and have registered the ammount received from customer (10.000 USD), which leaves an open balance of 1.000 USD.

I tried the go find "Uncathegorized ammounts" on the bank account where I registered the movement, but there are not uncategorized transactions, and I'm not able to match the balance of this company as a customer and as a supplier.

Can anyone give me a hint? This is desperating!!

P.S. - I would easily make a manual jornal with movement from accounts receivale to Accounts payable, but Zoho don't allow that.