What I am understanding from your post:
You are looking to have the audio have its own timeline in Hype so You can create your animations in sync with it.
e.g. A two minute audio will have a visible presence on Hype's timeline that runs for two minutes.
What I have done in my projects is to convert my audio to an ".mp4" using QuickTime 7 Pro (what a great editor!) - other programs would suffice I'm sure. Note: Make sure the file does not have an audio suffix - i.e. ".m4a".
Now what we have is a video (but no visuals) that shows up in the Hype timeline in a linear fashion. Of course You can add more audio ".mp4's" as desired.
Drag the ".mp4" audio file on to the Hype stage ("Animation pane"). A media player will then show up which you can drag off stage. With the ".mp4" file selected go to the "Element Inspector" where You will have the option to turn off "Autoplay" as well as hide the media player controls. However, hiding the controls does not remove its visible influence from the project, so I like to simply keep it off screen.
You don't necessarily have to keep the audio in your final output - it can be simply used as a guide during the creation process in Hype.
The audio ("AudioDemo.mp4") in the attached Hype Project started out in life as an ".mp3" which I converted using the process described above. The media player is off screen to the lower right. For the purposes of the demo I have the "AudioDemo.mp4" set to "Autoplay".
AudioTimelineDemo_JHSv1.zip (77.8 KB)
Note for future reference (not shown in the Demo): You can also have the animation synced to an audio media player's timeline for use on a web page. So the audio player is visible and dragging its timeline will also move the animation's timeline to match - or when playing - both timelines are in sync.