Please rename your Xorg.conf. Bumblebee has his own xorg.config, in /etc/bumblebee/ as far as I know named xorg.conf.nvidia
So you overwrite it.
Have you edit the /etc/bumblebee/bumblebee.conf
?
Driver=nvidia
[…]
## Section with nvidia driver specific options, only parsed if Driver=nvidia
[driver-nvidia]
# Module name to load, defaults to Driver if empty or unset
KernelDriver=nvidia-xxx
PMMethod=auto
# colon-separated path to the nvidia libraries
LibraryPath=/usr/lib/nvidia-xxx:/usr/lib32/nvidia-xxx
# comma-separated path of the directory containing nvidia_drv.so and the
# default Xorg modules path
XorgModulePath=/usr/lib/nvidia-xxx/xorg,/usr/lib/xorg/modules
XorgConfFile=/etc/bumblebee/xorg.conf.nvidia
For the xxx you mußt write the instalt Version.
Example (352 oder 340-updates)
Reboot. I hope I could explain it well and it works.
Source is a german Wiki for Ubuntu.