Seam preferences in JBossTools->Web->Seam should create a library in Java >Build Path> User Libraries and link that to new projects instead of copying the .jar files in to WEB-INF/lib, in should also enable the created library for deployment using Project->Properties->J2EE Module Dependencies.

Currently I have to do this by hand, and, if I am working inside Eclipse, this should be done automatically on project creation. This would make it easier to upgrade to a newer version of Seam.