QB Issue Resolution:

The invoice should be for the full amount of whatever class(es) he signed up for. Apply the partial payment towards the invoice and QB will keep track of the balance due.

Resolution for Issue 'How to do bookkeeping for a school?' available: Yes (Solved).
Source: Intuit Community forum.

How to do bookkeeping for a school?: 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 Invoice
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Error Recovery for Invoice [Canada]
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