You are confusing two different things.
If you file a schedule C for self-employment, you list all your income and all your "ordinary and necessary" expenses of your work. You calculate your net income (profit after expenses) and that flows to the rest of your tax return.
Personal itemized deductions (or using the standard deduction) is on schedule A and is completely separate from work expenses. Your personal deductions (charity, state and local taxes, medical expenses) have nothing to do with your work expenses.
