No, prevailing wage is the amount of money your boss agrees to pay you after you get your GC. So it is about the money you will get in the future, not how much you are currently earning.
As long as you boss is willing to sign such paper that will promise to pay you when you get GC, everything will be fine.
In my case, after I have served my company for 4+ years while getting the wage lower than MTA cleaning workers, my boss, aka SOB, declined to sign such paper even he agreed in the beginning. If such thing happens to you, then you are in trouble.