How to calibrate three orthogonal cameras？
Use an asymmetric calibration plate. Such as the new circle grid in OpenCV. Check here. You do not need to find the correspondences in the gui, but rather run the calibration directly. Also, do not forget to initialize the optimization problem using the median of the obtained poses. 

To calibrate multiple view setups, I would also recommend Multi Camera Self Calibration tool. It uses a simple laser dot and is much easier to calibrate, especially when the number of cameras increase. Of course, pay attention to the synchronization.