Start by realizing that no mechanical (rotating disk) HDD can move data between the mobo controller and the disks faster than the original SATA spec of 1.5 Gb/s - well, the best can get to 1.7. So there is no need to connect your 4 HDD's to a 6 Gb/s port - the four 3 Gb/s ports will do nicely, and the all can use the built-in RAID capabilities of the Intel chipset on your mobo.
The SSD, on the other hand, may exceed the 3 Gb/s rate of the older SATA version, so it should be connected to the first Intel SATA 6 Gb/s port, and you can boot from this device.
There are two additional ports rated at 6 Gb/s but provided by a second controller chip NOT part of the Intel system. The mobo specifically says these ports cannot be used for boot devices, and you are free to use them for data storage devices. I expect that the CD that came with the mobo includes among its many drivers to be loaded the one for this controller chip and its ports. Once this is installed after Windows is installed, like so many other drivers it will be loaded automatically from the boot device so the ports become available for use.