Yes use a fat32 formatter or I believe hp have one, you can't use windows format disk is too big.
There is also a command line option if you use ipodpatcher. I'm afraid these are all windows tools.
I believe you can do it directly on Linux but suggest you search the forrums and the rockbox site.
ipodpatcher allows you to write a complete Rockbox.ipod into the firmware partition of the ipod instead of the usual bootloader .ipod file
I think its better just to format the partion thus leaving the Apple firmware intact.
do note you will, under both sysetms have no Apple OS.