I can not help with your VAT or your multi-currency situation, but this is the concept to get it done
create a dummy bank called clearing
receive payment on the invoice, and deposit to the dummy clearing account
use write checks, do not print it, on the dummy clearing bank account select the vendor, and as the account select accounts payable, enter the amount, on the far right of that line select the vendor name in the name column, save
bring up pay bills, select the bill, and apply the credit the check created, then pay the balance when ready