Ahh OK, now that I think about it, EFI explains why there was three, the EFI partition is logical and surrounds the others.
I am not positive, but I believe you can install windows per my recommendations above, with only that disk connected. Then once complete update the Intel RAID drivers and reboot to windows again, then shut down. Then reboot to the BIOS, enable EFI, then save/apply/reboot and enter the Intel RAID ROM and build the array and once in windows initialize the disk with disk management using GPT. And actually, that EFI BIOS setting may not even be needed now, since you are not booting via EFI partition, so try without it first as it's really meant to be enabled if you are booting via an EFI partition which you wont be anymore.
No, I believe you only need the EFI partition to boot via EFI, and the only reason it was placed on the C drive previously was because you had it enabled in the BIOS the first time you installed.
EFI partition and BIOS setting is for booting from a 2TB or larger GPT disk, which you wont be doing. So you can manually setup a GPT RAID array / partition post windows install, and shouldn't have any problems doing that.