Hi Jonathan,
Seam 3 is a set of CDI extension. Not a new version of Seam 2 framework actually.
So there are a few ways to create/configure CDI project in JBoss Tools.
1. You can use JBoss Central to create a new Java EE 6 application or any example project which supports EE 6.
2. Create your own maven project with CDI dependencies.
3. Create a new CDI Project using New CDI Project wizard (New->Project->CDI->CDI Project)
4. Create a new Java/Web Project/... and enable CDI support for it (Right click on the project-->Configure->Enable CDI)
5. ...
Then just add Seam 3 jars into the project's classpath and CDI Tools will enable Seam 3 support automatically.
If you are using maven then adding Seam3 dependencies is enough for that (if you have installed JBoss Tools CDI Maven integration plugins of course)
See also https://community.jboss.org/en/tools/blog/2011/01/31/overview-of-context-dependency-injection-tools
http://docs.jboss.org/tools/whatsnew/cdi/cdi-news-3.3.0.M5.html
http://docs.jboss.org/tools/whatsnew/central/central-news-1.0.0.M4.html
http://docs.jboss.org/tools/whatsnew/central/central-news-1.0.0.M5.html