HDD + Modchip questions

[sublime90]

i have a ver 5 ps2 with a messiah 2 chip, i know you cant do both at the same time, but how would i be able to play final fantasy 11? what im asking is 1) how do i disable my chip? im used to just popping games in and they automatically load up (burned or not burned) and 2) say i disable my chip to play FF11, when i enable it to play burned games can i do so with the HDD still installed or do i have to completly remove it?

i allready tried and i cant get the HDD software to even load up (probably because my chip is'nt disabled)

any help is appreciated

thanks
sublime90