If you have a Slot-2 flash linker from the old days (think supercard lite and such) then rudolph's nds backup tool slot-2 is your best friend, otherwise he has other versions of the backup tool for wifi or ftp to suit your needs.
@KazoWAR - Will we be able to edit our boxes with this eventually, or is this not in the original source? Regardless, thank you for the translation work!
I seem to be having the same problems. Download cuts off halfway (around 1MB) if i didn't use an accelerator. But I think this is true for all downloads on this site right now (I've had the same issues with your box organizer and pokemon generator)