I'm also waiting for my FPGA ARCADE to arrive, but I've been using a Minimig from 2008.
So I suppose it will work like the original Minimig core: you'll be able to select one or two HDF files in your SD card and the core will boot from the master one if you provide a KICKSTART ROM wich has the IDE driver (3.1 from A600 or A1200).
You can create the empty HDF files however you like (I simply dd them in Linux) , but you should partition and format them in the FPGA Arcade with the OS 3.x install disk (not sure if it's mandatory but I believe it is).