on the tiapp.xml define:
<transparent-background>true</transparent-background>
on css define:
<style type="text/css">
html, body {
background : transparent;
}
</style>
on your javascript call:
<script type="text/javascript">
Ti.UI.currentWindow.setTopMost ( true );
Ti.UI.currentWindow.moveTo ( display.width-your.app.width, display.height-your.app.height );
</script>