You must file Form 8889 if any of the following applies.
You (or someone on your behalf, including your employer) made contributions for 2007 to your HSA.
You received HSA distributions in 2007.
You must include certain amounts in income because you failed to be an eligible individual during the testing period.
You acquired an interest in an HSA because of the death of the account beneficiary.
If you do have excess contributions to your HSA then they are placed back in your income for the year. Generally, you must pay a 6% excise tax on excess contributions. See Form 5329, Additional Taxes on Qualified Plans (including IRAs) and Other Tax-Favored Accounts, to figure the excise tax. The excise tax applies to each tax year the excess contribution remains in the account.
You may withdraw some or all of the excess contributions and not pay the excise tax on the amount withdrawn if you meet the following conditions:
You withdraw the excess contributions by the due date, including extensions, of your tax return for the year the contributions were made.
You withdraw any income earned on the withdrawn contributions and include the earnings in "Other income" on your tax return for the year you withdraw the contributions and earnings.
Basically, you will need to add the amount of contribution back into your income (Form 8889 is used for this). The amount your employer paid is generally on your wages already but again the Form 8889 is used to show all activity for your HSA.
I hope this information is helpful to you,