It appears that you have discovered an omission of income after you have filed a prior year 2006 Tax Return. This clearly means that you need to amend your 2006 Tax Return.
If the error was not due to an omission of income but due to some mathematical error, usually, the IRS service center may correct errors in math on a Tax Return and may accept returns with certain forms or schedules left out. In these instances, a taxpayer need not amend your return!
However, your specific situation involves an omission of 1099-Miscellaneous Income on your 2006 Tax Return. You need to understand that a copy of your 1099-Misc income has already been reported to the IRS, via a 1096 Annual Transmital letter sent by your employer.
The implication here is that it is only a matter of time before the IRS will send you a notice requiring you to pay penalties and interest on the omitted income that was reported on your 1099-Misc Income.
I would strongly advise that you do file an amended return prior to receiving a notice from the IRS to avoid at least incurring the penalties and interest of not reporting the income. By voluntarily filing an amended tax return, you have a very good chance of abating the penalties at least and possibly the interest as well.
Use Form 1040X, Amended U.S. Individual Income Tax Return, to correct your 2006 Form 1040 Tax Return. It would also be prudent to try and pay the tax by April 15 of the current year. The Form 1040X has all the Instructions and do select the correct service centers to mail your 1040X return.
The IRS wants you to "to enter the year of the return you are amending at the top of Form 1040X." Follow the instructions carefully and enter the information on the 3 columns as required. There is an area on the back of the form to explain the specific changes being made and the reason for each change. Be sure to enter a reason for change in income as being an inadvertent omission of income.
Further information on filing out an amended tax return can be obtained by clicking the following link below. http://www.irs.gov/pub/irs-pdf/i1040x.pdf