You can still store your keys in ~/.ssh as long as you don't use the default file names. By default, ssh will only announce id_rsa, id_dsa, id_ecdsa and id_ed25

You can still store your keys in ~/.ssh as long as you don't use the default file names. By default, ssh will only announce id_rsa, id_dsa, id_ecdsa and id_ed25519. But if your key for GitHub is stored in, say, ~/.ssh/id_github, it won't be offered unless explicitly requested with -i or the IdentityFile config option.