If you filed a return that you believe is correct, but the IRS has objections, you can't fix that by filing an amended return. You need to wait for the IRS to make a final determination, at which point they will send you a letter. You then have 30 days (usually) to appeal, and there will be a specific address and specific process to appeal the decision. You can't use the amending process to get around a final decision, you have to use the available appeal process.
