How to compile HDD to use PSX and PS2 games on internal

Hi all, I have recently purchased a fatPS2 to which I have installed free mcboot newbie pack.
What I would like to know is how do I set up the file/folder structure so that I can play PSX and PS2 titles from the same HDD (over network adaptor) I have even seen that you can store PSP and DVD/AVI rips in folders but the tutorial I watched didn't specifically show/tell you how it was more how to play PSX titles from popstarter via USB.

Any help will be greatfully recieved.