While the error distance introduced by the distance between transducer and head unit is minimal. The greatest error is broadcast via the GPS system. It can vary by up to +/- 3 meters in any direction. Your mark could be off by 10' in any direction even if everything in your boat was perfect and had zero error. The waypoint is a general location. To find the spot you need to scan or use a triangulation method. While DI or 2D are great tools, they also have limitations. They will only see at best the diameter equal to the distance to bottom. If your in 10' of water, your only going to see 10' (5' either side of the transducer) at a time. If your in 30' of water you will see 30' of water. You literally have to pass over the waypoint to see it and greatly increase the odds of spooking the fish. Not too mention your sonar will have trouble seeing though the prop wash you just created.
For me, the best option is to set my Side Imaging to read either the left or right side and pass the mark about 50' off to the side, make a 3/4 loop and pass the mark again at 90 degrees from the first pass. This gives me two points of reference and I can move in closer to drop a marker buoy. To elaborate- Cruise past about 50' to the right side of the waypoint with my SI set to read on the left side of the boat. Once I go passed my target turn to the right (away from my target) and make a loop so I can cross my wake and see the waypoint at a 90 degree angle from the first pass. Kind of like the old Clover-Leaf interstate on-off ramps. The benefits are you don't create prop wash in your fishing hole and don't spook the fish. Plus you can make a box around your target, not a circle, to find the exact spot.
I also like to start out fishing away from the spot to pick up any fish hanging around the outside edges, then work my way in slowely to the target. This is my method for open water submerged targets.
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