I just want to make sure I keep all my user preferences. When I install the updated version of blender, how can I keep all my user preferences?
As far as the Start-Up File, save a version as you like it in the older version and open it in the newer version and set it as the start-up file. You find that in the File menu by selecting "Save Start-Up File..."
I don't know about the User Preferences as I have the same question myself.