I use QuickBooks desktop to track income and expenses. Then I use TurboTax to file as sole proprietorship. When I import my QuickBooks company file into TurboTax, all of my income is already listed in TurboTax.
Then, as I add 1099 to TT, they increase my income above what it actually is. So, I'm showing double the tax liability on the reported 1099 income.