It depends on the location of the GPS antenna you are using. Are you using an external antenna or an internal one.
When you mark a waypoint .... it is marking the location the GPS antenna was at when you mark it. As Rickie stated, if the antenna and the transducer are not close to each other, the waypoint won't be accurate.
If you some something on the screen (an object seen by the transducer) and mark that when the transducer is directly over it ..... what you marked is the location where the GPS antenna was.
So, if you are at the bow and the antenna is close to the transducer, you will not introduce much error since the xducer and the antenna are close to each other.
If you move that unit ... with internal gps ... to the console, but the transducer is on the stern .... there is quite a distance between the 2 devices and the waypoint will have that distance of inaccuracy built in when you mark a waypoint.
In all cases, the waypoint is marked where the gps is located when pressing the button.... and if returning to a marked waypoint with the unit in a different location .... if you arrive at a location, it will be where the gps is.
The gps will also have some amount of position error that can't be controlled and will depend on the amount of satellites being tracked by the gps.
Hope that didn't confuse things further.
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Looking for the one that makes it all worthwhile.