Just tap the base you want to run when you have a runner. You have to tap before the pitcher enters the pitching motion. Also, if you want to cancel the stolen base sign, you can cancel it by tapping it again.
In this image, there are only runners on the first base, but if you want to run more runner, you can tap all the bases you want to run.
The color of the base that is instructed to steal will change, so you can see where you signed it.