[i presume] most payroll systems have acheckbox for deduct help per employee.
When you fill in your tax dec you would tick the box that says help debt and your employer would then tick the box that says yes deduct help.
then afaik it will automatically deduct once you are over the threshold.
so 47k is the threshold at the moment so your taxable income would need to be $900 per week for it to start being deducted (i think)
then it is 4% of your taxable income.

if you pay an amount back but then your annual income is lower than the threshold, it's too bad - you dont get it bacl... but better than owing it at the end of the year if you did go over the threshold.

i only work with one piece of software so im not 100%, but is this what you meant?