you got it a little bit mixed up right now
you need to format your card and put the update file AND the EOS on the SD kart.
now IF you are updating with the supercard ds lite than start it and start the update. IF you are updating with your 3ds than RENAME the update.dat file to updateb.dat and leave it on the error screen for 5 minutes.
you can also download the tool in my signature (3DStool) and start flashcard operations from it and follow the instructions