BizTalk 2006 makes it easy to add multiple binding files to an Application. By adding multiple binding files to an Application, you can easily select environment specific settings during deployment.
So if you have a Dev, Test, and Prod environment you can have three binding files all built into the same MSI package. Of course, you need to create and maintain multiple version of your binding files in order to use them in this manner.
To add multiple binding files to an Application, just follow these steps.
1. Export your binding files using BizTalk Server Administration (you'll need to change your setting for each environment).
2. Once you have all the binding files, inside BizTalk Server Administration add them as a Resource to your Application.
3. Add each Binding file and specify the Target Environment name.
4. Repeat for each Binding file and make sure the Environment variable is set for each file.
5. Create your MSI for your Application.
6. When you import your MSI on another Environment, you will get a selection menu to select what binding file you want to use.
I've put together a simple sample to show this. It will not actually run or do anything. It is just intended to show how to set up multiple binding files.
Download: Multiple Binding Files in an Application