The basic hypeDocument APIs are always for the top-level scene, so running them would affect whatever the current scene is. As an example, if you needed to continue the main timeline of the current scene from a button press within the persistent symbol, the code would be:
hypeDocument.continueTimelineNamed('Main Timeline', hypeDocument.kDirectionForward, false);
The second way would be to trigger a custom behavior in the persistent symbol. Then each scene would need to have custom behaviors defined for that particular behavior name and they'd essentially also do the same thing; this would require a lot of repetition but no code.