It is a straightforward process to do this.
To process a deduction via Payroll by Reference:
Click Payroll, and then click Payroll Entry by Reference.
Use the Transaction Type drop-down and select Deduction.
In the Reference field, double-click and search for and select the deduction via Reference number or description.
Click Select and then press the Tab key.
Double-click the worker column and find the worker.
Click Select and then press Tab key to move across to Input and type the amount to deduct.
Press Tab key to move to the Effective Date column and type the date for the deduction.
Leave the Retain check box unticked.
Review changes to check they are correct.
Click Exit.