I agree with Wayne. My approach is to not try to correct the underlying tables in Sage 100. If you need to electronically file, I believe (since I actually don't do the work around here!) that you can edit returns on their face in Aatrix. Something I have always thought was a great feature. Fix the employee's W-2 first by correcting taxable wage amounts and the taxes they compute, keep the employee's total withholdings the same by reclassifying withholding taxes to cover changes in fica and medicare taxes. Run the adjustment through the W-3 and the 4th qtr 941 manually as well. Finally, make sure the sum of all 4 qtrs. 941's equals the W-3...otherwise, the client will get a letter from either IRS or SSA depending on the direction of the error.
Tax professionals do need to be consulted unless your it. If the adjustment is significant, the executive involved could have safe harbor or tax planning issues because of the unexpected change in FIT. I DO NOT recommend keeping the FIT the same and the employer paying the difference unless that's is what the tax professional is wants or is willing to defend. Paying someone's withholding is a taxable event, and then you get into a never ending circular reference.