Normally you would have a @RemoteServiceRelativePath annotation on your GWT-RPC service. This tells the generated RPC classes to access the service under GWT.getModuleBaseURL() + RemoteServiceRelativePath#value(). If you are not fine with this default structure you can remove the annotation and after you have GWT.create'd the service just cast it to ServiceDefTarget and call setServiceEntryPoint(...) to set a custom path.
If you use RequestFactory you have to create a sub class of DefaultRequestTransport, overwrite getRequestUrl() and initialize your RequestFactory with this custom RequestTransport.
-- J.