God in Everything

I know the Bible says that in everything we need to thank God. But I found it really difficult to understand that God allowed even bad things to happen and that we ought to thank Him for that too. The other day I was going through a book by Catherine Marshall called "Something more". In that she too expressed the same problem.But as I was reading through I came across a vision someone had shared which sort of cleared out few things for me. It said , the lady in her vision saw darkness all around her, which is the filth,sin of the world and then a light approached her that surroundng her like a thick blanket and everything around her including the miseries, sickness, death, sin, and the viles. And it seemed to say "This is the presence of God". So she concluded that the presence of God surrounds everything around us and ofcourse ourselves and unless He decides to move out a bit, nothing can change its course or come near us. That was bit comforting for me becuase lot of unpleasant things happened in my life that caused me to question God and feel bitter inside of me. Now this sort of explains that He really was in all this. And God causes all things to work together for good for those who love Him and are called according to His purposes.