Hi there,
It's important that all your payroll information is set up correctly for your employee's pay to be accurate. QuickBooks Online Payroll is a great tool able to help you pay your employees by either cheque or direct deposit. I can provide some information about salary.
Unlike hourly pay which can have multiple pay rates, there isn't an option to add multiple salary rates for salaried employees. I can see that this would be a feature that you'd like to see to help with payroll. I recommend leaving feedback in the system by clicking on the Gear Icon, then Feedback. The comments made in that section are considered by our developers when designing new features for the software.
If you have any other questions, feel free to reach out here.