All you have to do is to mail a "Form 1096-Annual Transmittal Letter" to the appropriate IRS Address as shown on Form 1096, (the mailing address is based upon your State of business).
When you mail Form 1096, include the amended or corrected 1099-Misc and check mark the Box that indicates "Corrected". This is shown on the upper side of the Form 1099-Misc.
The corrected 1099-Misc is all you have to include with Form 1096 and since it includes the check mark X against the "Corrected" box, this will tell the IRS that you are including an Amended 1099-Misc Form.
There is no check mark required on 1099-Misc Form.
Not to worry, you have to amend the 2008 tax return and report the additional income. Clearly, you would be penalized by the IRS for the additional tax liability. They will generally charge you interest and penalty.
Generally, a good CPA can abate these penalties for you provided you have a reasonable reason for excluding this income. I would not wait for the IRS to get back to you and instead file an amended tax return as soon as possible. By doing this, the IRS will most likely abate the penalties.