Hello and thank you for your question.
The first step is to fix the employees' paychecks. Open them up in Quickbooks, edit them, and save them. You may have paid them too much, in which case you can eat the difference or collect it from you employees. Increasing tax withholdings will reduce the net paycheck amount, so to offset it you can maybe reduce federal or state income tax withholding, but do so at your own risk (it's not technically a proper fix, but easy). Alternatively, the proper fix (and the only one I can recommend) is to increase the net paycheck back to what it was prior to recording the tax withholdings by running an employee loan amount through the paycheck. You'll then show an amount due from your employee on your balance sheet for the overpayment.
Step two is to make any additional tax payments, if applicable. This would only happen if you already paid your taxes. For example, if you already made your EFTPS payment for Form 941 which was due by 1/15/16, and you find that you have underpaid because you didn't account for the additional withholding necessary, then you must schedule another payment. The same goes for any taxes due on the DE 9 Form for California.
Step three is to amend any necessary tax forms, such as Form 941 or for state withholding, if needed. If you haven't filed the forms yet, then you would have nothing to amend, so step three may not be applicable.
You'll be able to print your W2 Forms simply after correcting the paychecks in Quickbooks. The social security tax withheld from any employee is 6.2% of the employee's Social Security wages. The Medicare tax withheld from any employee is generally 1.45% of the employee's wages (employees with over $200,000 in Medicare wages have an additional 0.9% withheld).
Assuming you correct everything, it shouldn't affect your employees taxes.
If you have trouble with the above, you should consider contacting Quickbooks for assistance and if need be a local professional that can come and straighten out your books. I realize Intuit advertises that life will be easy if you buy its products, but in the same way buying a set of tools won't make me a mechanic, buying Quickbooks and its do-it-yourself payroll program won't make you an accountant or a tax professional. Truly walking you through every step of this would be difficult without being able to see what was done in your books and would probably take an hour or two of my time if you need amended tax forms and payments (it would be quicker for me to fix it than walk you through it). Normally I charge over $100 an hour... I do in any case hope this pointed you in the right direction and I sincerely ***** ***** question.