Raid 1 is absolutely a industry standard practice for the boot drive of a server IF that server is not a VM on a cluster obviously. As far as how raid should be implemented, the RAID card on the mobo is not a hardware raid, it is infact a firmware raid and not at all much better than the windows software raid on modern hardware. RAID 1 is an extremely low overhead operation. If you were talking 5 or 6 where parity calculation is involved, I would agree, hardware offloading is important.
We are talking about a server here, manageability and reliability trump speed. either way, the other replies are correct, you need a clean drive the same size or larger than the primary drive to establish a RAID 1 on windows. if MOBO RAID is to be used, the creation of the volume will indeed wipe the drive contents.
Another solution to think about, depending on the hardware and your needs, is to install esxi and virtualize the windows os. makes for snapshots and management less dependent on the hardware failing, as storage of the vm is already safer from failure than a physical install.
Either way, Raid 1 is no backup for data damage, only drive failure. Windows server has a very good backup feature set ready to be installed as a service.
https://technet.microsoft.com/en-us/library/cc770266(v=ws.10).aspx
Let me know if you have further questions.