employment income

Hi,
I’m too confused with employment income. My question may sound ease for many people, but I do not understand the following:
In the first and second chapters of BPP, we are informed that individuals pay for the income tax and they use employment income as a component of a scheme for calculating taxable income and then payable income tax. But in the third chapter we are introduced to the employment income and allowable deductions, such as: qualified travel expenses, contributions to registered occupational pension schemes, etc. I cannot understand when these deductions take place and who makes these deductions?