Let's ensure that no payroll runs are processed for those two months in QuickBooks Online Payroll, Darin. I'll discuss the details below.
If you process payroll for only one month in a quarter, you'll pay taxes solely for that month. No taxes are due for skipped months, and quarterly forms will report wages only for the months payroll was processed.
You can check out this article to file Form 941 in QBO Payroll: Pay and file payroll taxes and forms electronically in payroll.
To ensure timely filing, we recommend reaching out to the IRS for the guidelines on the process and what forms you need to file.
Let us know if you have any additional questions about filing tax forms in QBO.