Filetype plugins for foo filetype are sourced in that order:
1. $HOME/.vim/ftplugin/foo.vim. Be careful with what you put in that file as it may be overridden by $VIMRUNTIME/ftplugin/foo.vim -- under windows, it'll be instead $HOME/vimfiles/ftplugin/foo.vim
2. $VIMRUNTIME/ftplugin/foo.vim. Like everything under $VIMRUNTIME, this file should not be changed.
3. $HOME/.vim/after/ftplugin/foo.vim. This file comes last so it's the ideal place for your filetype-specific settings.