If you want to use region three, you have to put the 3ds rom into the sky3ds (it works better if you use only 1 rom from other regions per sd card because you won't be able to see it when you insert the sky3ds into the 3ds). After you have your rom, sky and 3ds ready, you go into "download play" application (you have to turn on wifi and be connected to the internet in order to use R3). Press the home button to go to the home menu and without closing the download play app, go to the 3ds online tools address through 3ds browser (
http://gbatemp.net/threads/release-custom-rop-loader-html.379531/)
3ds online tools. Then select region three and the game will start.
PD: This is the easiest way for me, as you don't have to change anything on the 3ds or SD card.
PD2: It may take a while for the game to load, be patient.
PD3: you have to run region three everytime you want to play a game that is not from your region.