Well basically the ps2 is like a computer and like a computer you have to have software to tell it what to do, you add the hardware ( ps2 network adapter, HDD ) like a pc, them a software like HD Advance tells the ps2 what to do.
Like upon loading the HD Advance disc after you have turned on your ps2 that is it will send a command to power up the hdd of the ps2, and show the splash screen on your tv, then when you add a game to the hdd with HD Advance you choose install game and when done naming etc you take out HD Advance disc put in game disc and when ready you choose ok and it sends a command to the ps2 motherboard to copy this game to the destination which is the hdd, same when loading a game to play from the menu it will check the hdd to find game by command and then load game, this is basically how it works.