You can clone the repository wherever you want. (I like to keep it in ~/Projects/dotfiles, with ~/dotfiles as a symlink.) The bootstrapper script will pull in the latest version and copy the files to your home folder.
git clone https://github.com/bhundven/dotfiles.git && cd dotfiles && ./bootstrap.shTo update, cd into your local dotfiles repository and then:
./bootstrap.shAlternatively, to update while avoiding the confirmation prompt:
./bootstrap.sh -fSuggestions/improvements welcome!