When you create the web project you can select for configuration "Dynamic web project with Seam". This will enable seam support for your project. To change the seam configuration right click on the project and select "Seam settings" node.
What you say is only causing to create another project with seam structure.
My main problem here is that I have to create eclipse projects fitting under our naming conventions and try to keep the project structure as close as possible to Maven.
This brings us to second problem of course, after Seam Facet default project creation, if I go and modify the project name and change the source/resource folders, JBoss Tools and Seam get crazy, I start receiving exceptions....
I am not copying the stacktrace here but if anybody is interested...