Yes it is. Remember, you're PSU also acts and exhaust fan too.
The test I do is if I'm checking to see if the case is getting a good ratio, I'll take a piece of paper and put it over one of the fans. If its an intake and its holding the paper to the case or an exhaust fan and pushing it away from the case, then its working the way its suppose too. If its doing the opposite, then the ratio is off and one needs to be flipped.
I got the Corsair H50 and the instructions said to use the rear fan as intake and my front fan is also intake. My top is exhaust.
So is it okay to have 2 intakes and 1 exhaust?
It's OK. The idea is to have the intake airflow volume be somewhat similar to the output. If the input is greater, then you have positive pressure which is good if you have intake dust filters. Also, you want the air flow to be smooth in one direction. In this case, from bottom to top.
I do not think it matters. The third pin is a speed sensor. Software such as Speedfan can control the motherboard fan speed. Possibly your cooler has supplied a program to monitor and control speeds also.
I have a question about where to plug the pump pin into. The instructions say to plug it into any 3 pin on my mobo.
Does it matter whether it's the CHA_FAN or the PWR_FAN? They're both 3 pins.
Dose not matters man plug it anywhere as long it is fitting fine.....you can even get some extra fans in there just cut any fan line and extend a parallel connection through it......simple boss!!!.....i hope you got it....just be careful not to short circuit any line or else you'l mess up everything.......