QB Issue Resolution:

You receive the invoice in full. Then deduct the fee on the make a deposit screen. Entering a negative number. That should net the deposit to what is paid.

Resolution for Issue 'How to post a “processing fee” accessed by customer’s A/P system. Example: We invoice services for $1,000. Customer pays $950 ($1K-$50 Fee). How do I post the $50?' available: Yes (Solved).
Source: Intuit Community forum.

How to post a “processing fee” accessed by customer’s A/P system. Example: We invoice services for $1,000. Customer pays $950 ($1K-$50 Fee). How do I post the $50?: 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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