How do install the OS on a secondary drive in a new Mac Pro?

For a general user adding a new drive to a running system with data, you would boot into the Recovery HD (which is just a lightly hidden bootable OS on an additional partition) during boot by holding command+R when you hear the startup chime.

You can then use Disk Utility to partition the new drive. At that point, you could clone the system from the HDD to SSD or run the OS installer and have a clean OS on the SSD so you can choose what user accouts, user data and apps you migrate over.

In your case, there is nothing you really need on the main HDD. I would delay erasing the HDD until you get the OS running on the SSD and see that the three iLife apps are still available for redemption.

Once you redeem those Apps - they will be tied to your Apple ID whereas the OS reinstalls are tied to the CPU serial number.