If it doesn't already exist in TurboTax, it is best to create your Schedule C prior to entering your Form 1099 that you need to link. Also, if you are filing a joint return, you need to make sure that the Schedule C and Form 1099 are both for the same spouse. When you enter your Form 1099, there is a screen on which you will "Select the business that generated this income of $X,XXX". Mare the correct business and click continue.
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