If you look on the demo page (http://fabien-d.github.com/alertify.js/), all of the alerts get injected into #alertifylogs.alertify-logs which is positioned by css and therefore should be easy to overwrite:

    .alertify-logs {
        position: fixed;
        z-index: 5000;
        bottom: 10px;
        right: 10px;
        width: 300px;
    }