Company expenses that are reimbursed to employees through payroll are generally setup as after-tax allowances in Attache payroll. These don't need to be reported on the Tax Certificate but sometimes there may be FBT implications. Refer to: Allowances and reimbursements | Australian Taxation Office.
Set up an employee expense Allowance
Go to Payroll, Setups, Payroll, Allowances, Maintain.
Create a meaningful Allowance Code.
Enter a suitable Allowance Description.
The Type can be set as Value.
The Tax Status is normally After Tax.
the Tax Certificate code is normally 0 = Do not show on Tax Certificate.
the Amount can stay as 0.00 and Variable so that individual amounts can be entered on timesheets as required.
Super is not normally calculated on after tax allowances. Leave the Include in OTE box unticked.
Complete other fields as required.
Click Accept(F9) to save the new allowance code.