Realise this is a bit old now, but wanted to share my recent experience with Ubuntu 12.04 since it's relevant.
Using the package manager (i.e. running the commands listed in the OP), you are required to install package dependencies as usual. These include the nvidia graphics drivers. If you have already installed drivers using a .run file downloaded from nvidia, they will be overwritten.
Using the .run file to install cuda, you are given the option to install only cuda, leaving your pre-existing drivers intact.
For some reason, on my system the nvidia-331 module listed as a cuda dependency is broken. Installing it leaves my system unable to boot. Therefore, the option to install only cuda was very useful, because it meant I could source my own drivers from nvidia.