Amg,
Multiple apps are ok. There's a few things to note:
* You can have the Page Tab for your 'main' app go to any URL from your site, not just the home page. You can configure that within Autotune, or the Facebook Developers area. The Site URL must be your home page, but the Page Tab is a separate setting.
* If you create other apps, JFBConnect won't be able to change the template on the fly. Our custom template override will only work for the main app. However, if you assign a template to a menu for a specific page that will be used only with your app, that should work just fine.
So, what your doing sounds just fine. When a user logs in, they will be logging in to your 'main app'. Other apps for different Page Tabs is absolutely fine as well, but users won't be able to login to those apps.. just the main one. Obviously test, but I think you're just fine if I understand everything correctly.
Hope that helps!
Alex