You'll need TurboTax Self-employed to take your self-employed write-offs, which reduce your 1099 income. You can also enter your W-2.
You should enter your 1099-misc, in full, and then enter your write-offs as well.
After you setup your self-employed work under Business Income & Expenses the software will walk you through all types of write-offs. Your business write-offs should only relate to your self-employed work.