In the old days of the panoramic process, the pano dialog actually allowed you to place images manually to give the alignment algorithm a hint from which to start. That disappeared a while ago. Now you need to import your images into layers, move the layers around to your liking, select the layers upon which you want to operate and then use the Edit > Auto-align layers... and Edit > Auto-blend layers.
As far as stacking goes - you may still need to align the images (for registration prior to merging, say, for focus stacking or HDR/luminosity masking) or even freehand for creative exposure blending or artistic blending. It all depends on what you are trying to accomplish.
As asked already - what is it specifically that you are trying to accomplish? There are a lot of different methods for aligning and blending or compositing, etc. other than what I suggested above.
kirk