If you do not agree with a Notice of Determination (which indicates whether you owe any tax, fees, penalties, or interest), you may appeal by filing a petition for redetermination, or you can pay the amount due and file a claim for refund.
There are specific deadlines that must be met for either of these remedies, and for that reason alone it is advisable to retain legal counsel. Missing a deadline can prevent you from recovering any amount to be refunded to you, even if you are otherwise entitled to it. For example, generally, after a Notice of Determination has been issued to you, there are only 30 days for you to file a petition; and if you do not meet this deadline, your tax liability will be final—and you will be required to pay that amount. That said, if you happen to miss the filing deadline, you can still appeal the liability by paying the tax amount due and filing a refund suit.