“ Do I need to file a 1040X with the exact same amounts?”---->Yes, you do; needless to say,you always should report the correct amount of income. So, go ahead and file your amended return. You’ll need to wait about 8 to 12 weeks for the IRS to process your amendment, and in the meantime you’ll receive your refund check. you can file an amendment at any time if you owe additional taxes. The time limit is three years from the original filing deadline if you want a refund. So, you may submit the 1040X along with the corrected 1040 and a copy of the 1099-MISC statement. Then mail it to the IRS along with your payment. As long as you file this by April 15th, there won’t be any penalties or interest.
“ How will this affect my state taxes?”---> The state and the federal government both have the authority to audit your returns. Just because one accepts your amendment, that doesn’t mean the other one necessarily will accept it too. As long as you have your proof, thesupporting documents, to prove your numbers are accurate, you will be OK.
“ Does the state see all of what is reported on 1099 vs gross sales and rec.?”--->Yes, I guess so; In general, if the IRS changed your agi and other figures, it is likely that the state might also make the same changes. This depends largely on your state and how they process returns. So, you need to file your state amendment to report these changes and recalculate your state tax. In order to make sure the tax is recalculated properly, you will need to know what exactly was changed (for example,in your case, they’d change a figure for income or for a deduction).
“ Do I need to file an additional tax return for the (wi) state?”--->Yes; as said above.