By removing the old disk while you install the new OS, will make sure that you don't format it by accident :)
If you set the disks correctly, it will boot from the primary first, so you won't have to worry. What would be a good bit of 'housekeeping' though, would be to (when you're all set up and running) copy all the old stuff you want to keep , to the 'new' disk, format the old one and chuck the stuff back- so you get rid of all the old system files that you don't/won't need, and free up space.