How do I not double expense payroll taxes? I pay & record the taxes each time I run payroll. Per QB, I have to exps fed tax (which I already did) creating the exp again.

I'm here to ensure you aren't going to double expense your payroll tax payments in QuickBooks Online (QBO), @annabelkroontje. This way, you can keep your account updated and make sure your transactions are accurate.

Based on your description of the issue above, it seems that your federal payroll tax is paid directly to the agency. You've received a notice from QBO saying that the said payment is late because you'll have to record it into your QBO payroll account as well. With this, you're informing the system about your payment transactions.

When you're recording a federal tax payment that was made outside QBO, you aren't going to double expense your payroll taxes. Then, there's no need to worry about the past two months of transactions that you've reconciled. This is because the process won't affect your books or your business accounting.

As mentioned above, you can fix the issue by recording the past two months of payroll tax payments in QBO. Let me guide you how.

1. Go to the Taxes menu.
2. Select Payroll Tax.
3. In the Payroll Tax Center page, select Pay Taxes.
4. Next to the Federal Taxes (941/944), select Record Payment.
5. Check, update, and enter all the necessary details about the payroll tax payment. 
6. Click Record payment. Repeat the same process for the other one.

I've attached screenshots below for your reference.

After that, I'd recommend pulling up a payroll report (i.e. Payroll Tax Liability). This is to verify that the federal tax payment is recorded accordingly. Just go to the Payroll section from the Report menu's Standard tab.

There are a variety of payroll reports available in QBO. If you wish to know each one of them, kindly refer to this article: Run payroll reports. It contains the complete list of available payroll reports, their definition, and the step-by-step guide in customizing them.

Additionally, you're already doing the right thing in reconciling your account every month. This is to make sure your books are accurate and effectively monitor your business payroll expenses. To learn more about it, you can refer to this article: Reconcile workflow in QuickBooks. Just select the link intended for QBO.

Please let me know if you have other concerns. I'm just around to help. Take care always.