Updating from 6.3.1

I am trying to upgrading an existing installation (v6.3.1) to the latest (v8.11). Onward I would like to update gitlab using the package repository described here using apt-get. I am not sure if omnibus was used on the existing installation (does it matter?). I do not see the omnibus gem installed so I’m lead to believe that it was just manually installed from source.
Can I just follow the instructions to update using the link above? Will it migrate all of my server settings and keep my existing git repositories? I’m running gitlab on ubuntu 12.04.5 with mysql.