It all depends on the kind of work you intend to do and the kind of technologies you are going to use. Furthermore, the use of IDE for server integration too is a personal/team preference. For example, I use IDE (Eclipse earlier and now IntelliJ IDEA) just as an editor. I don't use it to integrate any application server with it. i.e. no stop/start or deploy/undeploy operations from the IDE. Instead, I manually control the JBoss AS server. That's my personal preference. It's upto you and your team to decide whether you want to follow that approach or use an IDE to integrate the server.
As for JBossWS, I can't say much because I don't have the relevant knowledge in that area. Someone with more experience might be able to answer that.
Coming to the use of Seam in your project - this is going to be completely your or your team's choice and highly depends on the kind of application you want to develop.