You use the "Stocks, Mutual Funds, Bonds, Other" interview to report the sale. This interview is only available using "Premier" or above if you're using the online TurboTax products.
The loss is first applied against any capital gains. If there's still loss left over you get to use $3,000 of the loss as a deduction on line 13 against other income. Any loss left after that gets carried forward to be used in the following year.
Tom Young