QB Issue Resolution:

create a dummy bank account called intrade

receive payments on the customer invoices and deposit to the intrade dummy account

pay a portion of the vendor bill from the intrade dummy account and then pay the balance from your real account

Resolution for Issue 'I have a customer that is also a vendor. They apply what we owe against what they owe us and pay the difference by ACH. How do I enter this?' available: Yes (Solved).
Source: Intuit Community forum.

I have a customer that is also a vendor. They apply what we owe against what they owe us and pay the difference by ACH. How do I enter this?: this 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 issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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