Answer
In Lightning Payroll, the software automatically calculates and manages Study or Training Support Loans (STSL) based on employees' income. You cannot manually adjust this in Lightning Payroll. The ATO will perform its own calculations using your employees' income when they file their end-of-year tax return. This means that the extra amount processed through Lightning Payroll will be refunded to your employees and won't go towards repaying their debt.
Instead, your employees should make any voluntary repayments directly through their MyGov account, following the ATO's guidelines.