The IRS rules for reporting shareholder compensation require that you include in shareholder box 1 W-2 income and Form 1120S wages the amount of health insurance premiums paid for “more than 2% shareholders”. So, the W-2 from your S corp should have your health insurance amount in box 1, and reported as wages for the S corp, and the K-1 to you from the S corp should include the health insurance as Section 199A W-2 wages. If you haven't done this, you should file corrected W-2 forms and amend your Form 1120S to comply with the IRS rules. Note that only wages reported to the SSA within 60 days of the deadline are eligible to be counted as wages for QBI purposes.
If the S corp has any income left after deducting your wages, it is QBI income (assuming it otherwise meets the QBI requirements).
When you treat the insurance premiums paid by your S corp as described above (included in W-2, deducted as S corp wages), the health insurance is already deducted from the QBI of the S corp, and doesn't have to be deducted else where. "Bottom line" is that your health insurance is reported as income on your W-2, and then deducted as self-employed health insurance on Part II of Schedule 1.
If you only had Schedule C businesses, your self-employed health insurance would be deducted from the QBI, which is the IRS rule. Same rule for the S corp (self-employed health insurance deducted from QBI), it's just that when you report it according to IRS rules, it is already deducted from your S corp income.
For more information, see these IRS websites:
https://www.irs.gov/pub/irs-drop/td-reg-107892-18.pdf
https://www.irs.gov/newsroom/tax-cuts-and-jobs-act-provision-11011-section-199a-qualified-business-i...
https://www.irs.gov/pub/irs-drop/rp-19-11.pdf
https://www.irs.gov/businesses/small-businesses-self-employed/s-corporation-compensation-and-medical...
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