Hey, just because *I* don't know how, doesn't mean nobody here does.
I would *guess* that it's almost exactly like installing the Rockbox bootloader. You need a clean bootpartition.bin (or the original one you extracted when you started your rockbox install.) And instead of our bootloader-5g.bin you need the iPodLoader2's .bin file. Then you just use it in place of our bin, and that will *probably* work.
I make no promises, as I've never done it before. But it might.
Anyway, if it doesn't, you can reuse the clean bootpartition.bin and reinstall our bootloader anyway (or if you kept rockboot.bin, just do the last step to write it to your ipod)