Payroll Taxes due don't align with Payroll Settings

Thank you for reaching out to the QuickBooks Community, dirtzero! I am glad to see you here. Could you verify for me if you if you have exceeded the federal or state threshold? The IRS and state agencies may switch you from monthly to semi-weekly or weekly tax deposit if you meet or exceed certain tax liability amount and our system is programed to automatically reflect these changes. However if this is not the case, please let me know so we can investigate further.

To answer your second question, when you have an exempt unemployment account in QuickBooks Online, but unfiled returns still appear, it could be due to unprocessed forms from a period before the exemption was activated. You will need to manually mark these past returns as filed to clear them from your Action Needed list. You can record a prior tax payments in QuickBooks Online. I'll show you how.

1. Go to Taxes, then Payroll Tax.
2. Select the Payments tab.
3. Review the payments listed and locate the tax you want to record a payment for.
4. If the payment is listed, choose the option Mark as paid then select Yes, mark paid.

If the payment isn't listed, please follow the steps below.

Here's how:

1. Go to Taxes, then Payroll Tax.
2. Click Resources.
3. Choose Record tax payments, then Add Payment.
4. Select a Tax Type, then enter the following:
   • Period Start Date and Period End Date - the period that the taxes were accrued
   • Payment Date
   • Check Number (optional)
   • Notes (optional)
   • Tax Item Amounts
5. Once done, hit OK.

You can review this guide for more details about Recording prior tax payments. Again, please keep me updated as I will be looking forward to your response as we try to resolve these issues. See you in a few.