If I have a bonus that relates to the 12/13 Tax year but was paid after 6th April 13, which tax year should I pay tax in?
Note that the rule is when a person becomes entitled to payment of earnings. This is not necessarily the same as the date on which an employee acquires a right to be paid. For example, an employee's terms of service may provide for the employee to receive a bonus for the year to 31 December 2004, payable on 30 June 2005 if the employee is still in the service of the employer on 31 December 2004. If the condition is satisfied the employee becomes entitled to a payment on 31 December 2004 but is only entitled to payment of it on 30 June 2005. So PAYE applies to it on 30 June 2005 and it is assessable for 2005/06. The date that matters is the date the employee is entitled to be paid the bonus.
But why are you worried about paying tax. That is your employer's responsibility and they will do it for you. Ask you firm's finance department also for further clarification. HMRC are not an organization to mess with, they will tie up your life in knots.