Dear T. Gates,
If your employer has made an error on your W2, it is your employer's responsibility to correct the W2, and issue a new one to you, to the IRS and to the Social Security administration. The employer must file a W2c (corrected wage and tax
statement. Here is a link to instructions for an employee to follow if he notices that a W2 is incorrect: (page 5) http://www.irs.gov/pub/irs-pdf/fw2.pdf
Here are the acutal instructions for your employer to file the W2c:
I am not sure why your employer is stating that he or she owes you money, but if they do, and they pay you now, it should not be added to your 2006 W2, it should be recorded on a 2007 W2.
If you have already filed your 2006 tax return, you should file an amended return
once you receive the corrected W2.