Draw and be ready. That is it. If trouble comes your way, handle it as the situation dictates.
Don't be a hero unless there is zero possibility of innocent people getting hurt.
Your actions might well save a life, but it could also escalate the situation to a point where a bystander might get hurt as a result of you actions.
^This. You're not a cop, you have no legal right or obligation to use deadly force on a criminal just because he's committing a crime. Just quietly draw your pistol and hold it alongside your leg, out of sight and at the ready. The first rule of survival is to CYA, and protecting yourself from possible legal consequences for your actions definitely counts!
IF he threatens
YOU, or it becomes apparent that he's going to harm the clerk or someone else, then by all means act to defend yourself and the others. If he's just after the money and a quick exit, your best bet is to remain silent and be a witness.
Trying to be a hero because "fighting crime is the right thing to do" is absolutely stupid. You HAVE to think of your own life and what your actions will do to you and your family. What good will it do to you and your family if you get injured, killed or imprisoned because your ego told you to "get that maggot and take him off the street"? You really want your kids to have to tell people "daddy's in prison for killing someone, but he's a hero because he took on a robber. But we're barely making it, struggling to survive while he's in jail. I'm proud of him, but we're hungry and wish he were here for us." How would that make you feel?
Bottom line....the store's insured for their losses. If the robber doesn't appear ready and willing to hurt anyone, let him go. Don't ruin your life and the lives of your family just for the sake of being a hero. That's NOT what your permit and pistol are all about.
And FWIW, I was in that very situation once, but wasn't armed. I was in a store when it was robbed. Both of the clerks were between me and the robber, so I couldn't have acted anyway, and it was over very quickly. He took the money and a 6-pack and hauled ass.