What kind of 1099s? Interest and Dividends?
If you are using the desktop version you can go to forms Schedule B and when you're on the list go to menu item Edit and there should be a Sort Table selection.
May 2016 UPDATE
In the Windows Desktop program you can sort the dividends in the interview step by step mode just by clicking the Broker or Payer column heading.
So after you enter each 1099 or after a few you can sort them.
