The application.cfm file is run ever time a page is used within Savvy CM. Most of the time you will not need to alter this file. For those times that you need to you have a few options.
Application.cfm is encrypted by default. You do have other files you can modify which are included into the application.cfm and thus give you access to create variables and alter the Savvy default configuration.
When application.cfm is run it first reads a file called /actionfiles/config/applicationconfig_v[6|7].inc. This file contains code that sets the cfappliaction name, session management and timeout. Usually you will not want to modify this file. If you need to include variables or other code before CFapplication is run this would be the place to do it.
Do not put any code in here that references application or session variables. This is because those variables are not created until after this file and thus when the server restarts you will receive an error.
At the end of the application.cfm file another file is included. /actionfiles/config/endofapplication.cfm. This file is where you can add variables and other code. Normally if you need to add or alter the appliccation or session structures of savvy you would do so in this file. It also contains code for cferror. You can alter these or remove them based on your needs.