Calculate on 18% tax directive

If I do the calculation, I see I have to pay in a huge amount, is there no field I need to fill in, I was on a 18% tax directive

The directive only instructs the employer to take off 18% as PAYE, that does not mean your tax is set at that rate. Your tax is based on the total income less expenses and the PAYE deducted by your employer will be offset with the difference being taxable.

Does this mean that I will have to pay in that amount or does SARS calculate it differently when I submit my tax return

It means you will most likely have to pay the amount less the tax you paid. The SARS calculation does not take into account amounts already paid. Only when you submit will you see the net amount owing.