Load up your sidescan mosaic, in any of the recognized formats (Ozi, jp2, ecw) File - Add - select......
Select create object - polyline - and draw around your structure, on completion - without trying to manually connect the two ends, simply
right click and hit "close polyline". Select Navico Bottom Structure as the line type.
Now copy the line to the clipboard , Right click - copy.
Highlight the line and select "tools - modify - kind - convert to polygon ". Select Navico Bottom Structure (There are 4 different patterns defined)
Now Paste your outline back from the clipboard - ctrl v.
This area can be activated / deactivated in your Lowrance unit by selecting category "Fishing Ground".
It will appear as a transparent white area in "Transparent polygons" mode in GPSMapedit, so when working with these areas its best to use the normal display.