Can this help?

Salut,
If you are not married to your bubble footage for any reason you could use Foam to easily create your effect.
-Create some bubbles on a solid, duplicate and assign your logo to the duplicated foam effect as a texture et puis voila!
Check this example:
www.nyc-visual.com/eye.mov
If it's what you are after let me know and I will explain in detail or upload an AEP for you.
Hope this helps
Salut
Serge
www.nyc-visual.com