In Microkeeper, it's not recommended that you go back to update a previous Payrun.
Instead you can wait until the next Payrun, and either make the additional payment, or deduct the amount that was overpaid as an additional line on the Payslip.
If you did do an underpayment, the other option is to process a single Ad-Hoc Payslip, that only pays the employee the missing amount.