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.