I guess you mean a Mac Pro 2,1.
1) make sure that you have two super drives, the default config should only have one.
2) make sure both jumpers set to Cable Select
3) You can now use eject button to open the upper tray, and option + eject to open the lower tray. Or there should be a small eject icon on the menu bar to control them
And yes, you can clone disc between them.