If I recall correctly (I've only ran Flash, the program, once):

It has automatically merged shapes of same color into one. So to add or remove to a shape, you just had to paint in the same (or a different) color.

For what it's worth, I've found it super confusing.

Shapes of the same color are added to a single shape, shapes of different colors are extracted from each other. Lines (of any colors) can (but don't have to) split shapes. A simple rectangular selection with mouse can add a bezier point to a shape, simple aligning of the bezier point with its curve will erase it. If you know how to use the editor is is super efficient.