Zest and juice don't taste the same, so use whichever one you think will give you the flavor you want.
You shouldn't need to add any yeast in secondary, and if they're sliced you shouldn't need to poke them with toothpicks. If you decide to do them in secondary I would slice them and freeze them before adding them, that will burst the cells and make them give up their goodness more easily. You can zest them first too, if you think there isn't enough flavor already in the beer. I would definitely taste it first.