WindowBuilder is an Eclipse project and platform on which to build GUI design tools. At present, there are 5 examples of UI design tools built on top of it for editing the following types of UIs: SWT/RCP, eRCP, XWT, Swing, and GWT. The first four are part of the Eclipse WindowBuilder open source project and the last one (GWT Designer) is provided by Google.
GWT Designer started out as a standalone Eclipse plugin and part of the WindowBuilder family of products rom Instantiations. The original GWT Designer was independent of the GPE and did not need it to operate. All it needed was the GWT SDK to be installed and accessible. It also went beyond just GWT UI editing and provided many GWT development features (validations, launching, etc.) that overlapped with the GPE
As of GPE 2.2, the core GWT UI editing features of GWT Designer were integrated with the GPE. Overlapping functionality was separated out and not included with the GPE version. Support for various 3rd party GWT libraries like GXT and SmartGWT was also separated out (with the ultimate goal of having those vendors support their own components). The GPE embedded version is also much more "opinionated" when it comes to options and preferences, so many existing preferences were simplified, defaulted or removed.
Due to the fact that there are a very large number of pre-existing GWT Designer users who may rely on those extra features (wizards, 3rd party components, additional prefs, etc.), we decided to continue to build the full, standalone Eclipse plugin version of GWT Designer. The GPE version of GWT Designer is basically a subset of the full version. The full version includes the same plugins as the embedded version plus several additional ones implementing the extra features. The version of WindowBuilder available from the Google code site includes the full version of GWT Designer (as well as SWT and Swing support).
All versions are built from the same code base and can co-exist just fine. You can install the GPE and then install the full version of GWT Designer or WindowBuilder with no problem (or vice versa). This is the configuration that I use every day. If you do install the full version of GWT Designer, you will indeed see duplicate functionality in the form of additional wizards and launch configs, etc. I am not aware of any conflicts or problems installing them all together as long as you keep them in sync (e.g., don't update just GWT Designer and not the rest of WB as they all share the same core engine).
If all you want is the basic GWT Designer UI editing capability, you can get that just by installing the GPE by itself.