QB Issue Resolution:

The only way would be to create a separate invoice for the NSF fee

QB allocates the partial payment against all items on an invoice – you can not stop or alter that

Resolution for Issue 'How does QB Pro 2013 assign payments to different items on an invoice?' available: Yes (Solved).
Source: Intuit Community forum.

How does QB Pro 2013 assign payments to different items on an invoice?: 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.

Support for assign payments
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Error Recovery for assign payments [Canada]
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