Tranquil will be your best source of information regarding your hardware and how to configure it. I assume you've got their BBS2 barebones server?
In general, though, you can't tell Windows Home Server to use a specific drive for a particular purpose. It will use the first drive presented in the BIOS as the system drive, and will use any other drives in the storage pool. So you'll need to figure out how to get the drive you want to install on to appear as the "first" drive. regarding the RAID array you wanted to isntall on, did you create the array before installation? This is required, as an array is not generally created automatically just because there are drives connected.
Also, I'll note that Windows Home Server installed on a server with a RAID array is not a supported configuration.
I'm not on the WHS team, I just post a lot. :)
