I think you mean you reported officer wages on line 7 of your form 1120-S but didn't actually prepare and submit the W-2 form to the IRS. If so, the best thing to do would be to prepare the W-2 and submit it. However, it will be subject to penalties since it will be filed late. You can protest that though by submitting an explanation of what happened if the IRS sends you a penalty notice and it is possible the IRS will reverse any penalties assessed.
You can use TurboTax Quick Employer Forms to prepare the W-2 form. You can complete Form 944 to report and pay your social security, Medicare and income taxes. You can use Form 940 to report and pay your federal unemployment taxes. You would have to check with your state department of revenue to see what your reporting requirements are for state unemployment taxes.
You will see a link to Quick Employer Forms on the File menu option in TurboTax Business, look for Create 1099/W2.
Enter your E-mail address. We'll send you an e-mail with instructions to reset your password.