Hello jmawle, if you are wanting to assign the replacement disk as a global Hotspare then you will need to login to the bios of the PERC card.  Once in the bios need to go to PD mgmt. Once in Physical Disk Management need to select the disk & choose Make Global HS.  This should create the new drive as a hotspare.   Please let us know if you have any other questions.
We have a MD1000 with Perc6/e and 2 virtual disks consisting of RAID 5 750GB SATA disks.  One of the hard drives has failed and I purchased a new one to replace it.  I think the one I purchased (from a Dell supplier) is actually refurbished because it shows up as foreign.  When I try to recover it, it just creates it as a separate virtual disk.  I want to set it up as a hot spare so that it will replace the failed drive, but I can't figure out how to do this.  Can anyone help?
New Disk shows as Foreign on MD1000