Standard Navision doesnt provide any link between customer and vendor. But this can be done in the following way instead of creating two identity as customer and vendor:
Raise a credit note on the vendor for the value of $2000 and the overall amount of the vendor gets adjusted. Put a note on the credit note for further reference as to why you have raised a credit note. So Invoice of $10000 gets adjusted against $2000 credit note and $ 8000 payment.