Lets start with mobo. I'm going to assume that its that Asus one mentioned in your other topics. Asus has very good software for custom fan control. However, it will only use temp sensor for CPU to adjust fan speeds. If you want to use other sensors on mobo, you will need to use Speedfan. If you want to use case ambient temp, you will need hardware based fan controller.
Anyway, connect all fans to mobo. Use either Asus Fan Xpert or Speedfan to setup fan curves. Speedfan has very good documentation to guide on making fan curves. For Fan Xpert there are several videos as tutorial. But its pretty easy to use.
As for 2 in, 1 out. That is considered basic positive air pressure fan layout. Its very efficient, quiet and cheap for basic builds.