With no instruments on the system (no camera, no lidar) you have one boresight. This is the relation of the GPS antenna to the IMU. This is set in the post processing software (Inertial Explorer or POSPac). A boresight consists of three lever arms and three rotations.
These values are constant if you do not move the antenna relative to the IMU/Snoopy. However, as you flip the box around relative to the vehicle the signs on the lever arms change and the rotations as well. There is no way for us to set these automatically in IE so in each configuration you use the scanner you need to remember how to set these values. Of course, if you flip the box upside down you will have different lever arm values as well but if you just change the direction from front to back then the offsets just change signs.
Now add the Velodyne scanner. This adds another set of boresight values. Again on our system these values don't change once finalized. However, we still need to know the general relation of the system to the vehicle so on the advanced boresight tab in the corrections area you may need to set the roll to 180 if you flip it and the heading to 180 if you swap it forward to backward relative to how it was boresighted. The pitch may have to change to 45 as well if tilted.