If you're just upgrading to a new version, as long as everything that was in your Gemfile was installed when you ran bundle install
then I wouldn't worry about it. Just re-install gems as you need them instead of bloating your system with gems that you don't currently need.
If you have projects that you are porting over to the newer versions of Rails and Ruby, you can just run bundle install
as the first step in upgrading the app to make sure its dependencies are installed.
Maybe someone could give you an yes/no answer for transitioning with RailsInstaller, but I'm trending toward using rvm and gemsets to have a cleaner, more focused environment for each project.
If you want to switch back and forth between multiple ruby versions, maybe check out the gem pik. You can use it to install gems on multiple versions of ruby so that they're available across them all.