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How do you show a payment adjustment on HCFA for time of service discount if patient want to send claim in?

If the patient is sending in the HCFA then usually that is because the provider does not have a contract with the insurance, so there would be no adjustment on the primary claim. If this is a secondary insurance claim, then the patient would attach the EOB from the primary insurance when filing the secondary claim.

We have a few patients that we are in network with, but they want the self pay discount and send it in themselves because of their high deductible. Yes they want to double dip. I know if I give the patient a discount, the insurance gets it too, from what I understand. It just doesn't show a discount on the HCFA.

That's because in most insurance contracts you aren't allowed to charge any patient different than another patient. And, if there is an audit and it is discovered, then you'll have to refund that discount to every patient that came in there for that insurance. You probably should reserve the self-pay discount for those that truly are self-pay if you want to do that.