"How do I avoid double counting?"
By using the correct basis when reporting the sale.
Your per share basis for stock acquired through an RSU is
(compensation created by the vesting of the RSU) divided by (GROSS number of shares that vested)
You enter the 1099-B exactly as it reads and then click the blue "I'll enter additional info on my own" button. On the next page enter the correct basis in the "Corrected cost basis" box. The correct basis is: (# of shares sold) x (per share basis for that lot.)
Assuming that the sales of the shares acquired by the ESPP were non-qualified sales, (a pretty safe bet since you say that the compensation created by the sales is reported on your W-2), then your per share basis for this stock is"
(discounted price paid per share) + ((compensation created by the sale) divided by (# of shares sold))*
You can handle sales of ESPP shares in the exact same was as described above.
Using the correct basis in reporting the sale avoids double reporting the income.
Tom Young
* this term is the per share discount you enjoyed when you bought the stock.
(SINCE THE DEVELOPERS CHANGE THE SECURITY SALE INTERVIEW EVERY SINGLE YEAR I'LL NOTE THAT THIS ANSWER'S DIRECTIONS ON HOW TO CORRECT THE BASIS FOR THE SALE PERTAINS TO THE 2016 INCOME TAX YEAR. I'M SURE THAT THE INTERVIEW WILL CHANGE IN THE YEARS AFTER THAT.)
