941s do not match the QBO GL

There is no shortcut to making the transaction register match Form 941, because Form 941 is built entirely on gross wages and tax liabilities. To make them agree, you'll need to reconcile against your Payroll Expense and Liability accounts, not the net bank payouts in the transaction register.

To do this, run the Payroll Summary report for the quarter, as the total gross pay here will tie directly to Form 941, Line 2. Then, run the Payroll Tax Liability report to see how much was withheld and accrued. These numbers map directly to Form 941 lines 5a/5c (Social Security and Medicare taxable wages) and Line 10 (total taxes).  

Alternatively, you can open the draft Form 941 inside QuickBooks Online. The system automatically pulls these gross and liability numbers, allowing you to cross-reference them against your General Ledger.

Let us know if you have any other questions.