Attempting to make sense of the bible

Yahweh isn't an upstanding figure of morality, if he was why did it kill every living thing on the planet, Genesis chapters 6-9 the "Great Flood" which is unverifiable. Now if say that you don’t believe that the flood actually happened then I would type that that I agree with you, but if there was ever a time, in the past that the complete surface of this planet was water it’d have been a lot longer time ago than the bible allows but that's enough about that particular part of the Genesis chapter I’ve still  got the first 5 chapters of the first sub book of the bible to go through before I get to Genesis chapter 6. 


So here goes...


Genesis chapter 1  the text surrounding verse numbers 1 and 2 It ia from the new international version of the bible:
“1 In the beginning God created the heavens and the earth. 2 Now the earth was formless and empty, darkness was over the surface of the deep, and the Spirit of God was hovering over the waters.”

Just out of curiosity did the man that was writing this passage mean the sky? Not the literal heavens? Because if it did it would make more sense elsewise you have just annulled your very own judgement day concept, which may just be my personal perception of your, or just another, nonsense story book. Just a quick recap of the tall tale so far God has already created the heavens and the earth and that is it and he is still in darkness and the spirit of god is hovering over waters which he hasn’t yet created, so he didn’t create water? If that is so it means that water was here, in the vacuum of nothingness which we (human kind, most of us) call space before the Universe began now honestly that is unbelievable. 

Now I shall stop at that if you have an answer to my question or you could answer either of my questions please type it into the comments spot below, or if you have any other comments that could help me in my quest to understand these scriptures.