No. Don't touch system files, ever.
Whatever you have done in /etc
must be done in /home/username
:
/home/username/.vim <-- the directory where you put your plugins
and colorschemes and stuff
/home/username/.vimrc <-- the file where you put your settings
The pathogen plugin should be there:
/home/username/.vim/autoload/pathogen.vim
The bundle directory should be there:
/home/username/.vim/bundle
The three lines should be in this file:
/home/username/.vimrc