generating stateflow from a matlab program using stateflow API

I am working on a tool which generates stateflow charts through a program. I am having trouble placing sub states inside a parallel state. The problem is sometimes the inner states are wrongly placed outside the main parallel state. Also when drawing transition between sub states lines the lines go out of the outer parallel state causing compile errors. Is there any API that ensures all the states stay inside. At least checks whether sub states are inside the main state.

A similar question to the above one is regarding self loop transitions in stateflow. How to make sure that a self loop is outside the state? I mean how to prevent a self loop from looping within the body of a state