Actually, I got some trouble figuring this out myself. But if you want to get some results on the lower half, you have to shoot a charged dual-form shot in the place that shot the beam when it is open just before it shoots its beam. To do this, you need to be close when it open. You'll see what happen when you do this, and you'll figure out the rest.
I thought the last boss was very difficult to, but you just have to come prepared : some plump perogi (3 or 4) to get rid fast of the first 2 forms, some (2 or 3) leeching poultices or anything that cures poison, the third and fourth forms are there for you to relax. Just put on your jelly costume, and you should'nt have to use a single recipe for those 2 forms. And for the last form, once you know how to kill it...
I think ending #2 is worth it : it adds explanations of what happened during all the game to ending #1
