Federal tax liability over 100K
If your company incurred a cumulative federal tax liability that exceeds $100,000.00 in a single payroll period (line 10 of Form 941 or line 9 of Form 944), the IRS directly debits your account. This article explains why a separate check paid to the IRS is in your QuickBooks Desktop payroll register.
You will undertand the reason for the IRS check.
You have incurred a cumulative federal tax liability amount that exceeds $100,000.00 in a single payroll period.
When any single payroll (or a combination of payrolls within a tax payment deposit period) has a federal tax liability amount that exceeds $100,000.00, the IRS requires the tax deposit to be made on the following business day. QuickBooks Desktop Payroll Assisted notifies the IRS of the liability amount, but the amount is actually debited from your account directly by the IRS.
The remaining state taxes, along with federal unemployment, are recorded on the QuickBooks Desktop Payroll Service liability check. This is a separate debit to your company's bank account.