We have your 6047R-E1R36N system:
http://www.supermicro.com/products/system/4u/6047/SSG-6047R-E1R36N.cfm?parts=SHOW
How we can connect the 2 internal HDD for OS, together with other HDD?
You would need to connect 2 internal HDD to onboard AHCI or SCU controllers. You can not connect to AOC RAID card.