You are not in any trouble! The W-4 for your employer just indicates how much tax you want the employer to withhold from your paycheck. It does not go to the IRS or dictate how you have to file. Just enter your W-2 exactly as it appears in your tax return. Going forward you can change the amount being withheld from your paycheck if you want to. New W-4 forms will be coming out pretty soon anyway, because of all the tax law changes.