This is a SEP IRA, not a SARSEP. (See page 7 of IRS Publication 560 for the difference.) To date, company contributions are 100%, shareholder-employees contributions 0%.  I also confirmed the SEP is set up under the business name of the S-Corporation to conform with the requirements of pub 560 regarding SEP IRAs. Current tax law permits the S-Corporation to contribute up to $54,000 or 25% of the compensation of the employee, whichever is less. Moreover, with a SEP IRA, matching is not required.  I think when you mention the "Benefits section" you are talking about QB DESKTOP payroll, rather than QB ONLINE payroll. I am using QB Online Essentials payroll. QB Online Essentials does not appear to have a Benefits section. When setting up company contributions in payroll deductions under payroll settings, QB ONLINE does support SARSEPs, but NOT SEP IRAs established 1997 or later. So although I would love to do this through payroll, it does not seem possible until they update QuickBooks Online Essentials payroll with this option.

Also, if one uses the write check function in QBO, and enter a liability account below, it will DECREASE the amount of the liability.