Answer
Allowances for individual employees can be entered under Employees >> Allowances/Deductions >> Allowances using the green plus icon.
If you have common allowances to share amongst your employees, you can create company allowances under Company >> Allowances.
If you wish to itemise an allowance separately within an end of year or Single Touch Payroll submission be sure to tick the Itemised? box when editing or creating your allowance.
If you wish to edit multiple pay allowances at the same time you can do so under Tools >> Retrospective Tool.