Deploy or Copy?
When changes are made to files in your commerce application such as commerce config files or your application config files, you would simply copy these files to WC_InstName.ear folder and get away with it. This was true up until version 5.6.x of WebSphere Commerce, whose backbone is WebSphere App Server 5.0. But things changed with WCS 6.0 and WAS 6.0.
With 6.0, when you manually copy the files - your changes will work fine until some fine day when your application is redeployed with new updates or if your commerce instance is updated with a new fix pack or a maintenance fix. With Commerce 6.0 and therefore WAS 6.0, you have to deploy the changed files using the admin tool such as WAS Admin Console or wsadmin. If you manually copy the file instead of deploying- two things may happen depending on the situation. One, if this is a new file that did not exist in the previous deployment, this new file will disappear after the next deployment. Two, if you updated an existing file, the changes in the updated file will be lost after the next deployment.
To deploy a file, in WAS Admin Console simply go to Applications -> Enterprise Applications and check selection for WC_InstName.ear and then click on the update button. Using this approach you can update the entire application(which you rarely do with commerce!), Single Module such as WebSphereCommerceSreverExtensionsLogic.jar or simply update a single file. When you are updating a single file - be prepared to provide a relative path. This relative path is relative to your WC_InstName.ear folder.
Pretty interesting things happen when you update a single file using this approach. In order to investigate what happens make sure to check the changed files list when you are about to save the changes to the Master Configuration.