Here are some tips from my experience ( limited)
from my experience once your project is setup, if you use the smartgwtee.jar in your class path( you are probably best creating a user library and include all the jars from the lib folder of the smartgwtee release), all will be OK. You actually still need the smartgwt.jar file (included in the smartgwtee/lib folder) as this has all the ui components, basically all the client side classes and the smartgwtee.jar has the additional classes to support the smartgwt server framework so you can do the code-less databinding using the ds.xml datasource config files.
The google->configure for SmartGWT asks you for a location for your SmartGWT.jar which is what you are referring to. This sometimes puts the SmartGWT.jar in the project folder along with the SmartGWTSkins.jar but I find it works without these as long as you have them in your classpath/buildpath.
When you configure a project for use with smartgwt using eclipse it will add an <inherit name="com.smartgwt.SmartGwt" tag to your projectname.gwt.xml file. Mine contains the following, I had to remove the inherit as it messed up a few other things, I assume that the smartgwtee inherit takes care of any dependencies.
Please note that all of this is SmartGwt related and not GWTDesigner so best to have a look at the SmartGWT forums and latest quick start guide for further help.
There are some other configuration tasks to do and I have not found a nice stepped guide but the WindowBuilder preference from Window->Preferences has a GWT sub tree that you need to point to the GWT library if you havent already done so through a wizard already.
Then to fire off editing I found sometimes you need to select a java file and right mouse open with and choose WIndowBuilder editor. Perhaps once this is done then open defaults to the WindowBuilder editor