In order to coordinate two or more plans via an electronic claim, the primary payment must have transactions that list the patient's responsibility, how much the primary insurance allowed, and then any payments and adjustments. All these must balance to leave the remaining balance as the patient’s responsibility. On occasion, payments are saved without these required elements, and once the claim has been transferred to the secondary payer an internal scrubbing error occurs.  

When you apply a payment manually you would want to post a transaction to the claim with the amount of the Patient Responsibility (i.e. Copay/Deductible/Coinsurance/Patient Responsibility) so that whenever the claim is transferred to Patient or Secondary, that balance is transferred as well. If your payment batch was saved without the elements above and your claim was returned with the scrubbing error "Incomplete Primary Payer Amounts Pmts + Adjst + Pt. resp must equal charges for xxxxx," Best Practices is to add these transactions in the Payment Application > Batch (associated batch if not released) or > New.