Once you've set up the policy for each leave type e.g. Annual Leave, you can capture past applications one by one, or simply adjust the balance for each person (way faster).
To change the balance for the current year, head to Leave => Employee Listing => Select the employee => click on Adjust Leave => click "Adjust Leave Balance"
For example, if the person has consumed 5 days of annual leave this year, under Quantity, input "-5.0" for this year (01 Jan 2017 to 31 Dec 2017). If there was any 'carried forward' leave from last year, it will subtract from that balance before deducting from the current year's entitlement.
If you wish to adjust the 'carried forward' amount displayed, apply the deduction instead to the previous year (e.g. 19 Jun 2016 to 31 Dec 2016). If, unlike the example illustrated, the person has been hired for several years, you have to deduct a greater amount - to offset any system derived carried forward leave from the year before e.g. from 2015 to 2016!
An adjustment can be used to add extra days of leave too! And this adjustment can be applied to any leave type that is eligible to the person.