Regarding the PS2 Emulation on HAN or CFW, there its no difference, as both use PS2 NET_EMU (PS2 Classics), but if you own a 60Gb (CECHA/B/C/E) Backwards Compatible PlayStation3, CFW takes full advantage of the PS2 Hardware inside, so you are running on a original PlayStation2 hardware.
Lets start with baby steps here, i know the PS2 Net_Emu (PS2 Classics) supports Config files, but since you console its on HAN (which i assume it is), i am not sure if these Config files can be loaded.