Commission for partners who are also customers

We have customers that are also "referral" partners.  I have created an "other relationship" so they are set up as both a customer and partner.

I have set up partner commission and this worked great.

Now, I want to pay the partner by crediting the payable on the partner account so it just deducts the amount from an open invoice we have for the customer record.  This would save us from  billing them, and them in turn having to pay us a separate cheque.

I was hoping I could create a credit memo from the payable I owe them..but at this point it looks like I need to just add the credit to the customer record manually and then journal out my payable.  Confused yet?  Anyone else have this situation where partners are also customers and use the partner commission?