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If the -i option is given then the identity file (defaults to ~/.ssh/id_rsa.pub) is used, regardless of whether there are any keys in your ssh-agent. Otherwise, if this:
ssh-add -L
provides any output, it uses that in preference to the identity file.
If the -i option is used, or the ssh-add produced no output, then it uses the contents of the identity file. Once it has one or more fingerprints (by whatever means) it uses ssh to append them to ~/.ssh/authorized_keys on the remote machine (creating the file, and directory, if necessary.)
chmod go-w ~ ~/.ssh ~/.ssh/authorized_keys
on the remote machine.