Based on the web service classes modeled with Rational Software Architect the generator creates a folder in the build/svr/gen/wsc2 directory for each web service class modeled. This is shown in Getting Started. (This maps closely to how Axis2 expects services to be packaged for deployment.) In that folder a properties file, ws_inbound.xml, is generated.
To provide a custom ws_inbound.xml file we suggest you start with the generated copy that you will find in the build/svr/gen/wsc2/<service_name> directory after an initial build. Place your custom ws_inbound.xml file in your components/custom/axis/<service_name> directory (usually under source control). During the build the ws_inbound.xml files are processed to allow for a custom file first, overriding generated and default values. See Inbound Web Service Properties - ws_inbound.xml for details of the property settings in this file.