There is no “yes, but” about it. You Sold this to them.

“how do I apply the payment to the invoice as well as a cost of goods account.”

You don’t; you are thinking of this incorrectly.

The Payment is against the invoice. The Invoice is going to list the product. The Product […]

Resolution for 'both areas issue: 'Customer pays for an invoice and reimburses business for a item in Cost Of Good account in same check. How do I apply this payment to both areas?' available: Yes.

The both areas issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the both areas issue yourself by looking for a resolution described in the article. If it is a complex both areas issue or you are unable to solve the issue, you may contact us by clicking here or by using other both areas support options.

For more information about resolving issues related to both areas in Quickbooks/QBO or to get support for the issue 'Customer pays for an invoice and reimburses business for a item in Cost Of Good account in same check. How do I apply this payment to both areas?', click the link below: