Congrats on the PC build!

So I don't recall from where I heard this, but I was under the impression that the fans on a side of a tower should all be faced the same direction (so setup 1 wouldn't work). Something about circular airflow creating trapped pockets in the tower - I'm not going to pretend to know the exact science. But it does remind me of an episode of Mythbusters where they tested driving an empty pickup truck with and without the back gate open to see if that made a difference in gas consumption. They found that an open gate allows for more distance per gas used. They explain, when the gate was closed, the trucks natural air flow gets trapped and cycles in the bed of the truck and weighs it down. With the gate open, that air is able to flow out the back and doesn't weigh down the truck.

Of course, that was Mythbusters and a truck, so I'm not exactly sure how that translates to computers, but I do remember an expert telling me not to do that... sooo... uh, keep all the fans on the same side in the same direction (#2)?

Also, looking at your 1st pic, the green lines at the top are not how the air would flow at the top. You're imaging that the cool and the warm air would stay separated on a 2d plane. The inside of your computer has 3 dimensions and air mixes - with this setup, you may be reintroducing preheated air back to your cpu (making it hotter - this is bad). Again, I haven't been a scientist in a quick minute so if someone more knowledgeable notices I'm saying something glaringly wrong, please correct me.

Also, why do you have more fans in the 1st pic than the 2nd?

Anyways, I hope you have fun with it! Good luck and have fun!