I recommend that you leave "Connect Island Rooms" turned on (and yes, this is available in Chief Interiors).  The program puts them in because having unconnected island rooms can cause a multitude of problems with room definitions which can affect things like living area calculations, floors and ceilings, room moldings, etc.   If you don't like where the program puts them, then just move them or draw your own and then you will be able to delete the ones the program automatically put in