I believe you can setup aliases in ssh_config where you specify the actual hostname and the key to use. Which is what I've used in the past to get the right key to just work with git (and gitolite).

    Host github-yipit-main
      Hostname github.com
      IdentityFile ~/.ssh/yipit_main_rsa

then just go about your merry way of:

    git clone git@github-yipit-main:/yipit/yipit-main.git