QB now has me recording my manual payroll tax payment in a different way. I recorded it but it is not showing up in my check register. Any one else have this happen?

Keeping track of tax payments is important in running your business, @ylouise. I'll help you ensure they're recorded in QuickBooks Online successfully.

I've got some tips to share with you to isolate your issue for today.

To start, ensure you're selecting the right bank account when adding the tax payment. Choosing an incorrect account will not display the payment in the register. Please see the photo below for reference;

If the chosen account is correct, I advise making sure the dates are accurate and that All is selected for the filters in your bank register. This displays all of the transactions that were made in QuickBooks.

That should do it!

For future reference, here's how you can handle payroll transactions in QBO: Run and customize payroll reports in QuickBooks Online Payroll.

If you need additional assistance regarding payroll/payroll taxes, you can always reply to this thread. We're here to back you and your business. Keep safe!