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My Bonus checks were paid to me separately than at least some if not all of my other pay. 

 

This is from Turbo Tax website:  (I changed the word separately to bold print)

 

If your supplemental wages are identified separately from your salary (as a bonus, for example), your employer must withhold taxes using one of the following two methods:

  • Withhold at the supplemental rate of 22 percent.

With this being said, does the Employer have a choice how much they withhold from the Bonus' even if they paid them to me separately from my regular pay etc., or if not how would the IRS and my State even know how to charge me the difference that wasn't charged me if that may be the case, if some Bonus and Regular pay are in one lump sum in Box 1 etc. on the W-2?