Since Payroll deductions are not actual payments that physically flow through SchoolLeader, you need to handle these types of payments in a special way. If you posted these payments into a "live" batch which contained actual payments (cash, check, etc.), the Deposit Batch would be out of balance when it came time to reconcile.
To get around this, always post all Payroll Deduction "payments" into SchoolLeader with their own unique Deposit Batch. This means, close the current Deposit Batch prior to entering your payroll deduction payments and then close that batch immediately after you are done. This will make the payroll deduction payments isolated from all other payments in their own Batch. You can then mark the Batch with a comment such as "Payroll Deduction April 3rd". The payment account for the Guardian / Employee will properly reflect the payment credits eventhough you received payment through a deduction from their paycheck.