Let me try and help explain with simple english..
What everyone is trying to tell you is that even though you are physically using your flash(es) off-camera, using the ST-E2 to trigger them in ETTL mode makes them operate exactly the same way as if they WERE physically mounted to your camera. In other words, however you're used to adjusting flash exposure, do the same thing. With ETTL, you would use FEC, or flash exposure compensation (on camera).
I have a feeling you think flash exposure decreased because you have the flash(es) setup to your side, and you're used to lighting subjects head-on. That's just my guess.. I apologize if I'm wrong.