In the clustered environment whenever you want to make any configuration changes your supposed to use WAS Admin Console and make those changes on the Deployment Manager, the deployment manager then takes care of Synchronizing those changes to all the nodes.
Please remember one important thing that the Deployment Manager will only synchronize changes under the config directory
In case of portal server there portal configuration service related files stored under PortalServer directory. So if you want to make any changes in these files you should always use WAS Admin Console. Those changes would get stored in resources.xml file under corresponding scope.
Similarly if you make any changes in wkplc.properties or wkplc_comp.properties or wkplc_dbtype.properties file you will have to copy those changes manually. Please note one more important thing that even in a cluster the wkplc.properties file will be specific to a server so you cannot copy it as it is to other machine. Instead you should copy the corresponding helper file from primary portal node and use it only copy necessary property values to the other nodes.