If you want to file your return with what you believe is the correct information instead of what is on the 1099-MISC, just substitute your amount for what is on the 1099-MISC when you enter it. For example, your form has $2,000 in box 3 for other income and it should be $1,000, Enter the 1099-MISC and input $1,000 for the box 3 amount. You will need to explain your change and include it with your return, along with a copy of the Form 1099-MISC and then print and mail your return with the attached explanation.
Instead of reporting the correct information prior to getting your 1099-MISC corrected, I suggest you file an extension and then file your return once you have a corrected form. If you file an extension you should complete your return to the point where it is ready to file except for the 1099 to determine if you owe any tax. If you do owe, you will need to pay on or before April 15th to avoid a penalty. The extension is only for the "tax return" it is not an extension of time to pay any tax owed. You could also file with the 1099-MISC as is, and then amend your return once the form is corrected.
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