(Solved) Trouble with Alpha nodes in Cycles 2.79

You are about 99% finished with your setup. You just need to plug the principled into the second slot of the mix shader, and plug the mix shader into the surface output node and you are done.

If you need to change how blender handles the alpha channel, then you can change those settings for each texture in the image editor. I recently helped someone with some texture issues. Maybe that thread will have some useful info: