1. Using a Virus A, B or C, the settings in Cubase will be saved but none of the settings will carry over into the synth. I think what you need is a Ti model
The Virus Control software will enable you to do tweek it in Cubase, move patches around and any changes will carry over into the synth.
2. I think what you are referring to is the "mixdown" option. Yes it works perfectly well and takes all your separate audio tracks and mixes them into one. The quality of the mixdown will depend on how well the separate audio tracks have been recorded and having a good soundcard and reasonably fast PC is essential for this.