R510 HDD 12 and 13 not an option for boot device

I have a Dell R510 that I am trying to set up the internal 2.5" drive bays labeled HDD 12 and 13 as boot devices. I am running FreeNas on this server. I am able to see the drives during the installation process, and successfully install the OS, but the drives are not detected during boot. I have been unable to locate any settings that are directed at those drive slots. Are these drive slots behind a hardware raid controller? If so, is there a way to bypass that. I have flashed my controller to IT mode to allow the 12 hotswap bays to be available as a jbod. Would this not encompass the two internal bays as well? I have tried in both BIOS and UEFI with no luck. Any direction would be appreciated.