Report the stock transactions on your tax return. Otherwise IRS will get the 1099-B's, assume your cost was zero, and send you a bill (yes you can get out of it, but much easier to avoid it in the first place). Also if you have a loss for the year, you can offset up to $3000 of other income.
E-filing (available thru Turbotax or Taxcut) will speed up your refund, as will direct deposit.