You can use IDE to develop, deploy the apps, for start/stop server use the command line utility. I'm pretty sure NetBeans5.5.1 you don't see the problem that you've raised in the beginning of this thread. I believe in NB5.5.1 they fixed something in NB code to take care of the startup (classpath) issue, so if you use NB5.5.1 as your IDE it should work out of the box, start/stop/develop/deploy etc.
[Message sent by forum member 'cchidamb' (cchidamb)]
http://forums.java.net/jive/thread.jspa?messageID=230490