I have a two hard drives Disk1 and Disk2. I backed up the C Drive of my Disk1 using backup software and restores that to Disk2. Now I have two active partitions, one of each drive. Which one will/should boot?
The system BIOS controls in what order attempts are made to boot from each type of device : hard drive, DVD drive, USB drive, LAN, etc.
Your BIOS may allow you to specify a specific hard drive, but most likely it will simply say "Hard Drive".
In this case, you'll have to consider which of your drives is "marked bootable". This configuration is generally done within the operating system. In most cases, the primary drive on the primary controller is booted first, followed by the primary drive on the secondary controller, and so forth.