I've managed to get 'physical' inputs into Giga to use Gigapulse as an effect from my hardware DAW (although it's not without clicks at the moment)... but I haven't been able to figure out how to 'rewire' outputs from Cubase SX to Giga's DSP inputs.
Hmm. I'm not sure it was set up to do it this way. I think it will only accept a physical input from a soundcard, not a 'virtual' input from your sequencer.
It sounds like you have the soundcard's physical inputs working (to some extent). If you soundcard supports it, you could route the audio signal out of your sequencer to your soundcard's physical output, routed back in to the input, and then into GS3 and GP. The m-audio Delta 1010 allows you to do this from it's virtual patchbay/router, for instance.