Self employed and payroll fee

I am technically self employed in construction, work through CIS, therefore work is sourced by agency and pay provided via agency's selected payroll company. Payroll company charge me a fee each week and I get confused which amount I count for my gross income. Please see example of my weekly payslip: Contracted amount/gross income: 500 Payroll fee: 20 Subtotal: 480 Tax taken: (20% CIS): 96 Net pay: 384 When I record my income for tax purposes, would I need to state my contracted amount: 500 or sub total gross (without agency fee): 480. Because if I account 500 as my gross, then add agency fee as expense, this expense position does not contribute in reducing my income tax at all..because HMRC will account that I had to pay tax from 500, which I did not do..as I paid tax from subtotal or 480, even my initial contracted amount (and it appears on payslip) was 500. I would appreciate expert explanation what is correct way to account for my income in self assessment.

Hi,
The gross profit is the sum before any deductions. This would be the annual amount of contracted income/gross income. In the tax return you then declare your expenses. This allows Self Assessment to subtract the expenses to confirm your net taxable profit.  
It is the net profit that is taxed and has National Insurance deducted from it. Do not forget to include the tax deducted from CIS.
Thank you.