Hi there, don't mistake my guide as making me an expert on bumblebee, but i'll try and answer your question.
1. The nvidia driver does not remove nouveau, bumblebee changes between the graphics card which includes disabling one driver and enabling the nvidia driver. Both remain on the system. The xorg.conf.nouveau does not matter as it is only called if you set driver=nouveau in the bumblebee.conf file.
2. You don't set nvidia to start at start up. The reason bumblebee is used is so you can benefit from the power saving of having the intel card in use when the graphics card is not needed. When you use optirun glxspheres64 (for example) the nvidia card is enabled which uses more power so that the graphicly demanding application has a performance boost.
3. Unless you have used optirun, the nvidia modules will not be loaded. For example, run the command lsmod | grep -i nvidia and you will receive nothing. Run optirun glxspheres64 and while it is running use lsmod | grep -i nvidia and it will display the nvidia modules are the driver has loaded to use the discrete card.