The game and OS are installed on the hard drive and after that you no longer use the cf cards on the mpu. In a nutshell.
1. Install card used to install new content on hard drive, i.e. game, bios update, OS.
2. OS Bundle will include an OS version, Game Manager version, bios version, though not necessarily all 3. It may also contain a bios that is not compatible with your MPU and it will state so.
3. Game this is self explanatory.
basically to install anything, you would put the install card in top slot, and whatever you are installing in bottom slot. It is a menu driven procedure with the new stuff to install on the left, and the current contents of the drive on the right. The default will install everything on the left that is selected by default, and erase anything on the right that would interfere (i.e. old game, os, etc). The install will install the new game after it erases the old one from the drive. It will then perform a clear. You pull all cards out, and reboot and follow the same setup procedure pretty much as an alpha 1.
The clear card will erase nvram and eeprom and you basically boot the machine with the card in the bottom slot, no other card is necessary. It will only clear nvram and eeprom and leave all contents on the hard drive alone. This is a good option if you just want to re-do setup and not have to sit there through the whole process of copying back the entire game.
The newest OS will run all previous games, so you don't need to downgrade the os. Once you update os and or bios, you leave them be and only install the new game.