From the website's installation instruction,
Does this needs to be done more than once, such as every time the 3ds is turned on (from being completely powered off)? I really hope not.
4. Initial SKY3DS:
Power on your 3ds console , hold to press red/blue button with finger, insert to 3DS Slot with your sky3ds , it will not display any game icon on screen. Pull out sky3ds and insert to 3DS again , the LED light will flashing fast, the game icon still doesn’t display. Again, pull out sky3ds and insert to 3DS, LED light flashing and turn off in few seconds, this means the first game save data has been read EEPROM normally from MicroSD card, you can play to enjoy it.
Does this needs to be done more than once, such as every time the 3ds is turned on (from being completely powered off)? I really hope not.