After an IRS examiner receives your documentation and makes a decision regarding proposed changes to your return, you have several options. You can sign the letter stating that you agree with the proposed changes, and then decide what payment method you would prefer to use, whether paying in full, applying for an installment agreement, or seeking an Offer in Compromise. If you don’t agree with the proposed changes, you should first try to negotiate further with the IRS examiner.
You may be able to persuade the IRS examiner of their mistake by providing additional documentation. You can also request a telephone conference with the examiner, where you or your tax attorney can explain your arguments.
If neither of these methods are successful, you may request an informal conference with the examiner’s manager. You may instead request that your case is sent to IRS appeals, which has the advantage of being an entirely separate department within the IRS. The appeals officers can evaluate the likelihood that the IRS will win your case if you end up filing a petition in Tax Court, and may decide to settle if it seems probable that you could bring a successful case.