All of the installation methods create the same final directory layout. The resulting Geronimo directory will look something like this:

The text files are informational only, and can be freely moved or removed. The directories are the interesting part:
Holds the JARs used to start the server and run the offline deploy tool
The hot deploy directory. You can copy applications here and Geronimo will try to deploy them automatically.
Presently, just holds a file pointing to the Geronimo web site for the documentation.
Holds libraries required to load the most basic parts of Geronimo -- the foundation (or "kernel") which in turn loads all the other application, resource, and service modules.
Holds applications and modules that can be run in Geronimo, as well as shared libraries which the application and modules can refer to. Not everything in this directory will be loaded -- each library will be loaded only when a module that uses it is loaded. You might add entries here for database drivers or libraries that should be visible to multiple application modules without being separately distributed with each application. The Geronimo deployment tools and the Geronimo plugin installer will automatically copy applications or modules into the repository when they are installed.
Holds a reference copy of the XML Schema definitions for all the J2EE and Geronimo deployment descriptors, as well as the definitions of all the Geronimo configuration files.
Holds some files pertaining to the runtime state of the server, such as configuration files, the default security realm, log files, the transaction log, etc.
None of these directories should be moved or altered. Only a limited number of files in them should even be edited (one example of an editable file is the properties file that configures users and password for the default security realm).