It is a known fact that the IRS has a system for appeals for people who refuse to concede with the outcome of the audit exam.
If your audit examination was conducted by means of personal interview by an agent from the IRS, then the agent will explain to you your rights to appeal. If you happen to oppose with the audit results, then you can request a meeting with the supervisor of the agent who interviewed you. If you still cannot arrive with an agreement with the supervisor, the IRS will convey to you a report on the adjustments as well as information on how to request for a meeting with an appeals officer. However, if you seek to appeal your case, you need to support your claim.
Aside from the exams, you can also appeal other things such as the penalties like the trust fund recovery penalty, OIC, employment tax adjustments, seizures, liens, termination of agreement as well as other claims that you are currently facing.
The conference is an informal meeting and you can do it inside the office of the appeals officer, by phone interview or correspondence. On the other hand, you can also represent yourself during the conference or you can hire a tax pro like a tax attorney or a CPA to properly represent you. If, however, you still cannot arrive with an agreement with the Appeals Officer from the IRS or if you do not want to make an appeal, in the first place, then you can always take your case to the tax court.
For more information regarding the process of making an appeal and to know how to hinder your interest from growing, then you can refer to the IRS Publication 5 (PDF), Your Right to Appeal and If you Oppose, How you can make a protest. As well as the IRS Publication 556, Claims for refund, Appeal Rights and Examination of Returns. Reading the IRS Publication 1660 (PDF), Collection Appeal Rights, also helps on how you can make an appeal to the collection actions.