Hello Stergios, this motherboard comes with two 6.0 gb/s SATA ports (blue), two 3.0 gb/s SATA ports (black) and two backpanel eSATA 3 Gb/s ports for external connectivity (red).
I recommend you to create the RAID 5 using the internal SATA ports. Something very important is that this RAID will run at 3.0 gb/s, since you are mixing the ports.
The operating system can be install on ESATA external drive, just make sure you have this ESATA drive set as the default device to boot. You will need a converter from ESATA to regular SATA.