It's known to the 3DS users that the ninjhax is a piece of software that allows you to run unsigned code on your 3DS and it means that your 3DS has been hacked and you can run any software you want including SNES,GBA…homebrew apps,games,tool  etc.
Preparetion of activate the ninjhax via the SKY3DS
1.SKY3DS flashcart from official reseller
2.homebrew starter kit
3.CUBIC NINJA 3DS game rom
4.A 3DS, 3DS XL or 2DS console with a firmware version between 4.0.0-7 and 9.2.0-20.(9.2.0-20 is better).

Now read the following guide step by step carefully.
Firstly,Using the DiskWriter tool 1.07 to flash the CUBIC NINJA to the micro sd card for SKY3DS.

Secondly,Unzip the homebrew starter kit and copy these files to the root folder of the SD card.

Thirdly,Using the SKY3DS and switch to the CUBIC NINJA.Start CUBIC NINJA on your console, choose "Create", then "QR code", and finally "Scan QR code".
Get NINJHAX QRCode choose the versions of your 3DS console.
This is the QRCode for 3DS 9.2.0-20u
If your 3DS system is 9.2.0-20U, you can scan this pic directly.

Last but not at the least,lick A, when your 3DS screen show these messages:

OPTIONAL – once the ninjhax is installed to your gamecard, just go back to the "QR code" menu and it'll run automatically!
OPTIONAL – you can now run homebrew apps on your 3DS! Simply drag and drop application folders into the "3ds/" directory that was created on your SD card by ninjhax.
(PS: you can exit the homebrew ninjhax by click the switch game button. Then your 3DS will return the normal home menu.)
Currently the homebrews has built-in some emulators. You can't play game backups via this card.
SKY3DS+NINJHAX is the best solution for your 3DS console.You can play free 3DS backups and homebrews.

Resources from SKY3DS official