The capital gains tax rate is zero for filers below an income threshold (see the link below). TurboTax will automatically apply the correct rate, even if it's zero.

Since you mention $3000, you may also be referring to the limit on losses.  You can deduct up to $3000 of net investment losses, and any excess losses can be carried over to 2017 and beyond.  TurboTax will apply this as well if it applies.

Ten facts about gains and losses