Hi!
I strongly recommend working with GlassFish when preparing for the certification for the following reasons:
It uses the JAX-WS reference implementation web services stack Metro.
This ensures that the things to learn when developing example programs etc. is according to the specification.GlassFish is very easy to work with with a very nice administration console, a web service testing tool etc.
If you also want to choose the development environment in which to prepare for the exam, I would suggest Eclipse before NetBeans, except when working with WSIT and WS security. This because the tooling in NetBeans is a little too good - in Eclipse you are forced to deal with things at a lower level. NetBeans has nice tooling for configuring WS-Policy, which you can use, since this is something you do not have to be able to do by hand for the test.
Also do take a look at my study notes if you are to go for SCDJWS 5 - they are available here on JavaRanch in the SCDJWS Links section. Except for a lot of practical examples, there are also references to specifications etc.
Best wishes!