Let's say you want to override adf connections.xml file for specific environment instance deployment.

1. Create a file called something like connections-overrides.xml and source control it along with your application. This file should be in same folder as connections.xml. In this file you can use properties where you need to replace environment instance or project specific values. Enter properties in the following notation: ${{PROPERTY_NAME}}. See Property Replacement Support.
2. Define the required properties on your deploy workflow, and set the scope to either Environment Instance or Project as appropriate.
3. Edit your deploy instance and associate your deploy workflow to it, if not already done.
4. Your workflow properties will now appear on either the environment instances or projects depending on the scope, and you can provide values for them.
5. In your deploy workflow, edit the deploy step and set the Override File Pattern (FDWLS_INP_OVERRIDE_FILE_PATTERN) property. The value is in format actual_file=override_file. For example, connection.xml=connections-overrides.xml.
6. At deploy time, the WebLogic deploy step will run property replacement against the override file using the properties you have defined, and then replace the original file prior to deploying artifact to WebLogic domain.

This can be done for any other files as well. For example, you can override web.xml, weblogic.xml, weblogic-application.xml files similarly. Alternatively, you can create separate override files for each environment as well and define Override File Pattern as expression to control which override file is used based on current environment from workflow execution.