Hi mate,
If you want to draw shapes on the same layer without them intersecting, enable Object Drawing mode. Then each brush stroke will become a separate Drawing Object and you will be able to retain the ones underneath intact.

Alternatively, you can create as many layers as you like with the little + button at the top left of the timeline and place your strokes on different layers.
Nick - Character Designer and Animator, Flash user since 1998 | Member of the Flanimate Power Tools team - extensions for character animation