The first step is to satisfy yourself that HM Revenue & Customs is correct in its calculation of a tax underpayment.
Once you have done this and agree that an underpayment exists you should make a payment on account. This should be sent directly for the attention of the investigation officer and not to the Collector’s Office or it may be posted as a general payment onto your Self Assessment account in error.
Making the payment serves the dual purpose of preventing interest from accruing on the amount and also serves as a sign of co-operation which may help reduce the level of any penalty ultimately imposed. HMRC can go back up to 6 years as a general rule of thumb and where settlement covers more than one year it will usually look for a negotiated contract settlement figure including tax/NIC, interest and penalties as the method to put things right.