Try Commissions and Rebate module
Why don't you have a look at the Commissions and Rebate module, and mainly the commissions part? There you can define your supplier as a relation and link him to your sls order to accumulate the acrued commission amount \the discount trhat is on quarterly basis\ see commission agreements parameters. While the line discount will just go with the pur order as you do it at the moment.
And in case you have a link with Finance you can precise the operation type that goes with these quarterly invoices \invoice, credit or debit note, etc\ in commisiion parameters.
I think this functionality might help you with this case.