Yes, you run the update file (as if it was a game ROM) and tell it to update, once it's done you shut the system off and the icon should have changed, and you can then run it on the 3DS.
Go through all of the 3DS's settings (including spotpass) and turn off all the automatic updates and content downloads, and don't let the 3DS have an internet connection.
However the 3DS will still try to get you to update in order to access the eshop and sometimes to play new games, and you can't get around that, just always make sure to update your flash cart BEFORE the 3DS.