sold a 2 family house used 1 unit as primary residence since 1999,rented on and of for 15 years the second unit

This is going to be two sales of property.  It will be based on the percentage that you set up for the rental vs personal.

You will need to enter the sale of the rental portion of the property through the rental section on TurboTax.  When it asks if you disposed of the property this year you'll say yes.  Then you'll enter the percentage of the sale price that applies to the rental as well as any costs that you had associated with the sale.  

You're going to have to recapture all of that depreciation.  So you're going to owe taxes on this portion of the sale.  The exclusion for a personal residence doesn't apply to this part of your home sale.

Next, you'll scroll all the way down in the wages and income section of TurboTax to "Less Common Income".  There you'll click start next to "Sale of Home (Gain or Loss)".  Then you'll enter the information about the percentage of the home that was your personal residence.  This portion of the sale gets that $500,000 exclusion so you're really just reporting the sale.  It won't change your income tax at all.

@166kniskern