New builds of Designer have support for Web projects. Web projects has "WebRoot" folder with WEB-INF, web.xml, libraries and output for "src" source folder also points on WEB-INF/classes. So, this is usual J2EE project.
So, in Web project your have web.xml wher you can write all what you want. GWT Designer provides extension to deployment process for Web project - you can configure which GWT modules to bundle with Web project.
Note, that Web projects can be deployed as WAR and as exploded directory.
See following images and try to play with GWT Designer 1.6.0 and above.