The distance between the unit and transducer will play a part but how much so depends on how far apart they are and how accurate the civilian GPS system is at that time. The GPS Receiver is built into the control head on the HELIX 5ci SI-GPS units.

Example: the distance between the unit and transducer is 8 feet. You are traveling due north and see some structure off to one side and mark it with a waypoint, the unit thinks that the GPS Receiver (inside the control head) and transducer are at the same location. If you come back to that waypoint also heading due north, there would be no additional inaccuracy introduced by the unit to transducer distance. The additional inaccuracy starts adding up if you come back to that waypoint from any other direction other than due north, with heading south being the worst case. Although the GPS may show that you are on top of the waypoint you will be up to an additional 16 feet off from the actual structure that you marked. Remember that this is in addition to any inaccuracy within the civilian GPS system. Most of the time though you should be within 2D sonar range though and you should be able to find that same structure again.