Actually, that link may have the diagram you are looking for. I have attached the specific image that I think will be helpful. If you look at bottom portion of the image that starts at $SPLUNK_HOME you can see the file paths to particular apps through the $SPLUNK_HOME/etc/apps path. Each of those apps will have a structure that is similar to the orange and green "$APP_HOME" diagram at the top of the attached picture where you will be able to edit your configuration files for a specific app (in the local directory which is at the right of the diagram).
It is important to remember the precedence of configuration files whenever making changes to them. Below is a link that explains configuration file precedence and a list of both Global configuration files and App/User specific configuration files.
As usually it depends. If those apps have any views/dashboards then those are installed on sh layer. Usually “apps” (aka TAs) w/o views are installed mainly on heavy forwarded (some time UF or IDX), but I think that there are also times when those are also installed on sh-layer too (e.g. fields definitions),
@vrmandadi... Same page has another detailed diagram.
If you want to create a Splunk App you can refer to the following as well: http://dev.splunk.com/view/webframework-developapps/SP-CAAAEUC