Hi there, @sjones2.
Let me provide some insights about how QuickBooks Self-Employed calculate estimated tax payment and help you from there.
The possible reason why the estimated tax increase than expected is that self-employed people have to pay both halves of the Social Security and Medicare tax. In contrast, a W-2 employee (your spouse) only pays one half, and the employer pays the other half.
It also increases your estimated tax if your regular transactions and business logs had missing deductions.
Also, I highly recommend contacting TurboTax Customer Support. This way, they can provide some advice on how to properly set your head of household in QuickBooks Self-Employed.
You might want to check out these articles to know how estimated tax payments calculated and Head of Household set up:
Please touch base with me here for all of your QuickBooks needs, I'm always happy to help. Have a good one.