I've noticed that the % withholding tax that that the payroll system applies varies widely for our commission employees who's gross pay fluctuates. Can I override this?

Hello there, jeff26.

Let's make sure that the employee has the correct tax information. This way, QuickBooks will calculate the correct withholding tax. Kindly see this article for more details: Payroll Tutorial: How to Turn on and Set Up Payroll

I'd also recommend contacting an accountant to be advised if you can override this. 

Please get back to me if you have more questions with this. I'd be around to help you further.