The record follows the case
Documents and explanations given during an examination become the foundation for everything that comes later. Appeals generally works from the examination file, and when significant new information appears for the first time at Appeals, it may be sent back to the examiner for review, which slows the case. Positions taken casually in an audit can be hard to walk back once they appear in an examiner's report. Treating the audit as the first stage of a possible dispute, rather than a conversation to get through, tends to produce a cleaner record.
Choosing when to escalate
At several points you decide whether to keep negotiating or to move the dispute forward. You can usually request a conference with the examiner's manager, ask for Appeals review before a formal notice issues, or wait for a notice of deficiency and petition the Tax Court. Agreeing to extend the assessment period can keep a case in Appeals, while refusing may bring a notice sooner. Each choice changes the timeline, the interest that accrues, and who on the government side is deciding the case. None of these choices has to be made alone, and most can be discussed before a deadline forces them.
One strategy across stages
Collection is part of the same picture, since an assessment that follows an unsuccessful dispute moves to collection, and collection hearings can sometimes revisit questions that earlier stages did not resolve. Penalties are another thread, because defenses such as reasonable cause depend on facts that are easier to document early. Interest keeps running throughout, which is one reason some taxpayers pay disputed amounts while continuing to contest them. Gather the returns at issue, all IRS or state correspondence, and the documents already provided, and work with your lawyer on an account of what was said in any meeting. We map where the case is now, the next decision point, and how today's choices fit the stages that may follow.