This article shows how to configure alerts.

Who can configure alerts?

Users who are member of "Prime Alerts Administrators" and having "Manage Web" permission can configure alerts for all site collection users. Generally, site collection owner's group members have "Manage Web" permission for site collection. 

How can I add an alert?

You can click on alerts icon (visible as * for versions 1.2.1 or prior).

That will show you popup to manage alerts as per the following image:

Anything that is added to Alert Message is shown to all site collection users until it is removed from here or user manually closes it.

Can I configure alerts for site and sub-sites in site collection separately?

As of build 1.2.1 Alerts are only possible to show at root level site (Root Web). If you go to the subsite and update alerts, it will apply to everywhere. This is a known issue and will be fixed in upcoming release.