QB Issue Resolution:

1099 income is called out separately on tax forms, but it is part of your company income, so for estimated tax purposes, just use the net profit number for your company.

I don’t use QBSE so any more help than that I can’t provide, it is just not ready for prime time IMO.

I find it more reliable to use the IRS form 1040-es which is free and has a worksheet that is accurate IMO.  A little head scratching and you can put it in an excel sheet to make it easier

Resolution for Issue 'QB SE Tax settings: How do I enter Social Security and pension 1099 income to get the correct tax estimate?' available: Yes (Solved).
Source: Intuit Community forum.

QB SE Tax settings: How do I enter Social Security and pension 1099 income to get the correct tax estimate?: 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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