The Shoto HDK implements the InvenSense MPU-6500 6-axis IMU. In order to properly design your tracked object, you must know the orientation of the IMU and configure the JSON file with this data. The datasheet for the MPU-6500 can be found here:
The IMU's axes are defined in the datasheet by the following diagram.
Note that the axes are referenced to the pin 1 indicator, shown as a dot on the above image.
Now that you know how the axes are oriented, you need to know how the device is oriented on the Shoto HDK. The image below shows the bottom side of the Shoto core module with the location of pin 1 of the IMU indicated.