QB Issue Resolution:

the system automatically calculates quarterly estimated tax amounts. You would not be penalized if you paid your taxes before September 15. For more information about the quarterly schedules, you can visit the IRS website.

After that, you’ll need to print the Form 1040-ES to record it as payment. Then, mail it to the IRS since the program is for recording purposes only.

Here are some helpful articles that will provide more details about estimated taxes:

Resolution for Issue '3rd installment of estimated taxes are due in September. Would I be penalized for paying a partial amount today and then the remainder in Sept? Thanks' available: Yes (Solved).
Source: Intuit Community forum.

3rd installment of estimated taxes are due in September. Would I be penalized for paying a partial amount today and then the remainder in Sept? Thanks: 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 Form 1040ES
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Error Recovery for Form 1040ES [Canada]
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