$ 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/objects/