Do bii arduino:settings to configure the new SDK path and the board as yun.
In this example we have unziped our SDK into c:/biicode_env/arduino-1.5.8.
$ bii arduino:settings
Enter SDK path (/../biicode_env/arduino-1.0.6): c:/biicode_env/arduino-1.5.8
Enter board (/o list supported options): yun
Using arduino port: COM13
And that’s all. Now you can use your Yun with biicode.