I just spoke to a friend who said that adding more fans won't really help a great deal if you have a CPU cooler, I can use one (probably pretty bad) fan from my old CM case. Will that be good?
One has nothing to do with the other. In order for the CPU cooler to cool well, it must have a constant supply of fresh cold air and for the hot air to be exhausted. Same goes for video cards and hard drives.
I wont be able to use 2 fans on the sidepanel, due to the Hyper 212+ blocking one vent. If I were to add two fans (meaning I would have to buy one) would it be best if I would use one bottom intake fan, and use the other for an extra exhaust at the top? This would mean that I would have a negative air pressure, I read somewhere that the CM 690 is better off with positive air pressure for temps... So should I buy no fans at all or only two? And not just one?
You would be better off with a positive air pressure, so put one fan in the bottom intake and one in the side bottom as an intake. But like I said, the 4 pack of 120mm fan deal costs as much as a regular 120mm fan, just go for it and you won't have to worry about fans for the next decade.
I vote for the 690 II Advanced as well. I am running just two fans in my system 1x140mm 96.5 CFM intake, and another exact spec as exhaust. Check out my video's if you want to see more. Newest Video I shot over the weekend http://www.youtube.com/watch?feature=player_detailpage&v=FFzt7DTkqpU Older video before CPU Cooler & Aero Cool Fans showcasing the wiring http://www.youtube.com/watch?feature=player_detailpage&v=7AjrGB7dSrc