Use the Nintendo Dev Interface with the files attached to get the SDK.
Put the Unity for 3DS folder into the environment folder.
Set up the environment. Make sure it is in the right location on the computer. The Window script file needs to be used.
Open a Unity project.
Put the code from the Unity for 3DS attached file into the license manager on the Unity Project
Help>Manage License...>Activate New License
Restart Unity. Go to build settings. and then you will see options to create a CIA
Then use Citra or a New system with CFW to run builds and the finished product.