I have tried both ways.
After the first reboot after updating via the software update panel it boots to a GRUB shell only.
I had this kind of error when i did first installation of SME7b9 to a MB with 2 SATA drives connected to NVIDIA-RAID. This controller defaults to RAID0, which is not what you want.

Had grub error after complete installation of SME, because installation wrote the files, but boot manager could not read it.
So you should check, if there is any onboard raid controller and if so choose pseudo-RAID1 (that is what i did) or choose JBOD.
Also i would advise you to lowlevel format both disks first.