I would absolutely suggest ProAnimator for your situation.
It's a standalone application, which can make movies with alpha channels for your AE 5.5 or any non-linear editor. It's also an After Effects plug-in. Even if it's not compatible with 5.5 (and I don't know whether it is), it is compatible with AE 6.5 and 7, to which you'll probably upgrade, one day, right?
You can download a demo from zaxwerks.com (click on the zaxwerks icon at the top of the page) and give it a try. I think you'll be amazed how easy it is to get very cool, complex animations.
By the way, you should have Illustrator to make the most of ProAnimator or Invigorator. Photoshop's export paths function will work in some situuations, but it's not the best choice.