You are correct that you can't report income net of expenses, and then also deduct the expenses.
As I understand you the amount on the 1099 is net of expenses that you are actually paying.
So you can either report more income than is shown on the 1099 and deduct the expenses you are paying, or report the income net of those expenses and not deduct them.
Either way, you should show the same net profit from self employment.
You should report your business in the way that you believe correctly reflects your income, expenses and net profit.
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