I use an exploded ear format (note I'm using JBoss AS). If I make web resource changes, I copy them over to the exploded war directory and the changes are immediate. If I make a java source change, I compile it and copy them over to the appropriate exploded directory, and then do touch on application.xml to force a re-deployment. I use ANT for all this stuff.
seam-gen sets all this stuff up for you.
Yes... I was using netbeans and I've never tried seam-gen before.
Now I'm moving my project to Eclipse...