Hi Danny,
you could do all little lakes and the big one in single steps and create your major and minor shapefiles step by step.
As a second step create your waters with only the shorelines step by step in RM and combine these outlines with QGIS to one single polys shapefile. With two lakes I had to manually draw a rectangle outline around my lakes. Save this new outline and let IMC generate your water with that outline and all your major and minor shapefiles.
edit: Just found this again ...
http://www.reefmaster.com.au/index.php/forum/feature-requests/37-export-boundaries-only#117
I tried this weeks ago for one map of two lakes, which contains additional islands. It also should work with lakes on an island, but I did not try yet.