First of, an android application is just an "archive" that contains a specific architecture.
As you pointed out, it is composed of a Manifest (xml) file defining the different parts of your application: Activities, Services, Permissions, etc.
There is also the resources files such as layouts, pictures and files used by the application.
Finally, there is the source code.
I recommend you take a look at online tutorials which are well detailed over the Internet, and to take a look at the Android SDK samples.
To develop Android applications, I recommend that you download the Android ADT bundle (containing both Android SDK and Eclipse IDE including Android projects management).