IRS sent me a notice of prior year taxes and interest due for form 940. I paid it. If I post to the FUTA tax account, will that mess us current year accrual amount?

The interest due will be in Interest Expense account.   The FUTA tax you owed  - is it for 2021 ?   If so; I would put it in a separate tax account - create something like " Prior Year Payroll tax".      That way when your CPA reconciles the 2022 payroll taxes in QBO it will match the year end payroll reports.  And this tax shows up on a separate line item.    He/she may put it all in the same place on the tax return; but it will make the review of your books clearer.