I think the fall exam will use the 2005 code, but check the NCEES website to be sure. I also work for a utility and had never really even looked at the NEC prior to studying for the PE exam. In my opinion the code questions are not super difficult, but mainly just time consuming to be able to sift through the book and find what you need to answer the question. Because of this, I highly recommend getting a copy of the NEC Handbook rather than just the code itself, because the added commentary in the Handbook proved very helpful and time-saving in finding the other sections of the code relevant to a specific question. It also helps if you have a head for the legalese and the bass-ackwards logic of the way the thing is laid out. I read somewhere (probably here on EB) that the NEC is "an engineering code written by lawyers".
In my case, I didn't worry too much about prepping for the code questions--since I was not at all familiar with it and given the study time constraints I had I figured it was more efficient to spend my study time on other topics. On exam day, I saved all the code questions for the end, so I didn't chew up valuable time trying to find answers in the code book. I'm glad I did because I was able to take the time to dig into the code book without feeling rushed to get an answer. I think I ended up taking about 45 minutes to answer all the code questions at the end.
There are others here on EB that spent a lot more time prepping for the code questions that may be able to give you more detailed advice. If nothing else I suggest checking out the Electrical Exam Prep forum and look for threads on the NEC.
