honestly I haven't used Enterprise Application Projects in Eclipse. What I have used was a basic Java Project which I packaged and deployed on Tomcat using Ant. If you don't know Ant don't worry that is pretty easy to learn. What you need to study a bit more is the way your application structure needs to be(because if you deploy as an ear the app has a different structure than an app deployed as war).
Create an Ear project, select to have it also auto create the War and Jar (I use the EJB3 form).
Crack open a Seam Ant created Ear file (booking example is a good one).
Lay out the files in the right bits (Ear, War and Jar).
Tell MyEclipse to "exploded" deploy it to JBoss and click on the button for the JBoss server inside MyEclipse to just run the server.
Simple as that... I have posted more detailed info that this elsewhere on this forum.
No ANT to build the project
No Ant Script to run the project
No ANT script at all.
You can hack away at the source and you dont even need to re-build/re-deploy the code... 99% of the time (notably when hacking with the .xhtml files) you just refresh the page and carry on... BLINDINGLY productive!!!