Generally speaking, I would encourage you to open the graphical editor by double-clicking on the SwitchYard icon vs. hunting for the switchyard.xml in src/main/resources or target/classes.   What's likely happening in your case is that generated configuration, i.e. config that is generated based off of annotations, is present in the version in target/classes and not in src/main/resources.

The goal for the tooling is to minimize generated config as much as possible and go with source config.  In that case, the version of switchyard.xml in both locations would be the same.  Even in the case where config is generated, we can likely smooth that out by encouraging people to view the application configuration via a double-click on the SwitchYard icon or something like Project -> View Configuration.  The idea being that if a user is drilling down into individual config files on their own, they are qualified as a power user and have a deeper understanding of the mechanics of our config generation.

It's in the Project Explorer tab.  In the screenshot you posted, it looks like you are in the Navigator tab.  You'll see a little SY icon in the tree right below Maven Dependencies.