I have been printing a lot of parts lately with multiple islands, and often get zits exactly where I want them least:

So, it would be great if you could add some geometry to your model which sets the point where new laters start, and/or tells the nozzle where to cross the island boundary during travel moves. What I have in mind is a geometry type which S3D recognises as an island-boundary crossing point. You would probably have to import it in a separate operation so that you could then tell S3D what it is. S3D would have a button like 'select layer-start geometry' and 'select boundary crossing geometry'.
Could be surfaces which intersect your model geometry:

Or could be curves on the surface of your model:

Or you could tell S3D to try to avoid selected areas. Perhaps you could paint your model within S3D to tell it what to avoid:
