This guy says that he gets 20C higher temp in R3 than in other gaming cases, pretty devastating.
Not really. Gaming cases are dedicated to high airflow regardless of noise considerations. In addition gamers typically overclock their CPU as a matter of course. They also tend to buy graphics cards which are factory overclocked and then overclock them even more. Put systems like these into a case with only one intake and one exhaust fan and of course you will see significantly higher temperatures. It would have been more useful if instead of simply talking about the need for extra fans the reviewer had installed some and said what the difference was. But given the flexibility of the Moduvent system it is possible, as has already been said, to remove fan covers and install extra fans until system temperatures are satisfactory.
Bear in mind that both the CPU and the GTX 680 will as standard both downclock and undervolt in idle situations. Under load, the CPU will overclock automatically (Turbo modes). There is a similar feature on the GTX 680. So you will need more airflow at load, but how much may depend on what that load is.
So, if I would to get 2 additional 140mm scythe slipstream fans for R3 what would be the best position for them and which way(intake/exhaust).
Yes, it would be sensible to plan for an extra exhaust fan in the top rear position, and an additional intake fan, preferably in the bottom position if the PSU will allow it. I would still recommend PWM fans because the system is one where you need relatively low airflow at idle, and substantially more at load. PWM fans will accommodate this automatically. The other options are to add fixed speed fans, or to use some form of manual fan control.
Also how can you tell which is intake and which is exhaust without turning them on?
If you look carefully at the fans, there should be airflow direction arrows moulded into the frame. Typically the fan hub is on the intake side and the air blows over the struts.