An employee can cash in up to one week of annual leave each employment year. There are a number of rules and restrictions regarding cashing up annual leave, which are covered this support article from MBIE - it's a good idea to familiarise yourself with them before cashing up annual leave for your employees.
To cash up annual leave in FlexiTime, simply create a pay for the employee and then add the Annual Leave Paid Out pay code to the pay. Enter the number of hours Annual Leave to be paid out and then select the Annual Leave Rate to be used. Note that this will be taxed as an extra pay, see the end of this article for more details.
If an employee has actually taken leave then always use the Annual Leave Taken pay code.
If you need to pay out accumulated Holiday Pay to an employee, for example if they are changing to Holiday-Pay-As-You-Go, please see this article.