@missjulia101  "But will I mess things up if I manually edit our weekly payroll for additional federal witholding ?"

Not really, but you have no reason to do so. If they want extra withholding, have them refill out the W-4 with an amount in the extra withholding box.

"Will QB charge me additional fees ?"

No.

Well, not for this specific reason, anyway. I'm sure they'll charge you extra fees somewhere along the line for something.

"do I need to submit additional paperwork to the IRS ?"

No.