With the growing use of Maven in enterprise projects, starting off with the best possible pom.xml is important. The good news is that there are a number of Java EE 6-related archetypes which can help you get started while offering IDE independance. The bad news is that their quality and portability in particular varies significantly.
The Java EE 6 platform APIs are now in Maven central : javaee-api:6.0 and javaee-web-api:6.0. These should be used with a
provided scope and your POM should contain dependencies for the actual implementation (check this 3.1 download page for how to work with GlassFish).
Consider using that simple platform dependency rather than replying on archetypes introducing a long list of dependencies mixing APIs and implementations.