QB Issue Resolution:

you book the full sale to  a liability account

You pay the labor/freight using an expense account

then on the check to the vendor

line one the liability account, full amount
line two your commission income account, your amount as a negative
line three, the labor/freight expense account, the amount as a negative

Resolution for Issue 'how to deduct commission income and freight charges in a bill from vendor' available: Yes (Solved).
Source: Intuit Community forum.

how to deduct commission income and freight charges in a bill from vendor: 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 Expense Account
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Error Recovery for Expense Account [Canada]
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