In most cases, the "first" disk of sufficient size will be used as the system disk. The "first" disk is determined by the BIOS, and different BIOS revisions and providers have different ways of making this choice, so you may have to fiddle
around a bit.
The usual answer is to make certain that your desired boot disk is attached to the lowest numbered SATA port on the primary SATA controller on the motherboard if you will have only SATA drives, or as master on the lowest numbered IDE port if you will have
a mix of IDE and SATA drives. If you have multiple SATA controllers (for example both Intel ICH# and JMicron controllers) make sure you connect to the primary controller. :)
In your case, I would make sure your system drive is the first disk on the primary controller, then I would wipe both disks (using e.g.
diskpart in another computer) and try again. In V1 it was relatively important that your disks be properly connected in the event of a server reinstallation; some scenarios could result in reinstallation/recovery not being offered as an option.
Finally, as far as I know, Vail will not offer the option of choosing a system disk at installation time, as part of the GUI.
I'm not on the WHS team, I just post a lot. :)
