If you want to use a smaller disk as the system drive, and have a pre-existing installation of Windows Home Server 2011, the following (unsupported) procedure should be useful:
- Move all shares and client backups off of the second partition to other locations (other drives) in your server.
- Remove the system drive from server storage.
- Delete the data partition on the old drive.
- Clone the system drive onto the new drive. (You could skip deleting the data partition, and just clone the rest of the drive.)
- Replace the old drive with the new drive.
Cloning the system drive is faster than restoring the server, in most cases. If you want to restore the server onto the new drive instead, after deleting the data partition, back up the server, then restore onto the new drive.
I'm not on the WHS team, I just post a lot. :)