So, you can run payroll summary reports from the report section that will give you the information you need. 

I ran the Payroll Tax Liability Report for June that SHOULD show the amount of taxes you will need to pay for the month. Then I did if for April and May too. I filled out the 941 online (from the IRS) and just followed the examples of the past 941 reports.

Then I changed the report date to the "quarter", to get the total liability for the quarter, which matched my entries on the form when added up.

The online version is different in that it has the added lines referenced above for COVID... so I am holding off as long as possible before I submit them. Like you, I prefer to do it through QB so I have it in my archives.