Salary staff who also need to be rostered separately

We have staff members who are on salaries for work completed. Of occasion they are also required to work shifts that require clock in/out functionality. The problem is, anytime this happens (even though we have multiple pay templates set up, in Roster Elf and Xero) it will overwrite their salary with the timesheeted hours, meaning that when posting a payroll we have to go back through the staff member's payslip and manually add in the salary hours/amount.

We need a way to have staff on a salary and get paid additionally for their hours worked outside of the salary.