# cd ~/annex
# cp /tmp/big_file .
# cp /tmp/debian.iso .
# git annex add .
add big_file (checksum...) ok
add debian.iso (checksum...) ok
# git commit -a -m added

When you add a file to the annex and commit it, only a symlink to the content is committed to git. The content itself is stored in git-annex's backend, .git/annex/ (or in direct mode the file is left as-is).