How to decide what window to open first in Titanium Alloy. You can remove all markup from the index.xml view (the file itself must be there!) and then create another controller based on your logic.

app.js

/* /Resources/app.js - Generated by Alloy, here to understand the flow */

var Alloy = require("alloy"), _ = Alloy._, Backbone = Alloy.Backbone;

Alloy.createController("index");

index.js

/* /app/controllers/index.js */

if (Ti.App.Properties.getBool('isLoggedIn', false)) {
    Alloy.createController("home");
} else {
    Alloy.createController("login");
}

index.xml

<!-- /app/views/index.xml -->

<Alloy />