Specify the new Startup Disk in:
System Preferences > Startup Disk
You can keep both drives in the machine, and boot the the other one when you please. To boot from a different drive quickly (but temporarily) hold down the Option key as you start up.
Many Mac Pro owners find a tangible speedup by establishing a lean, mean, Boot Drive, with only System, Library, Applications, and the hidden unix files including Paging/swap. Users are moved off to a second drive, and disk access to System files and User files speeds up a great deal.
This also makes system upgrades easier, because your files stay put and only the Boot drive get modified.
Japamac's blog: Make room for performance -- Moving the Home folder