I understand that you want to use your GitHub for Mac GUI, but if you were to commit your changes through the terminal instead, here is what you would do:
# Get the status of your working copy:
$ git status
# On branch Integrating-a-recommendations-textbox
# Changes not staged for commit:
# (use "git add <file>..." to update what will be committed)
# (use "git checkout -- <file>..." to discard changes in working directory)
#
# modified: assets/app/scripts/templates/popups/recommend.hbs
# modified: web/wgwt/models.py
# modified: web/wgwt/views.py
#
# Add each file you want to commit individually:
$ git add web/wgwt/models.py
# Or add them all at once:
$ git add "*"
# Make your commit
$ git commit
# You can also use the `--all` or `-a` flags during the commit
# to add all **tracked/modified** files (but not untracked files)
$ git commit -a
# To push the new commits to a remote repo, use the following:
$ git push <remote-name> head