Ok, let me explain a little. Our rejection was not related to the NOC code or anything like that. We just provided the wrong type of documentation for one of the areas. So they told us it was incomplete. We provided state police record instead of federal. An error on our part - that's what we provided when we came to Canada a few years ago with work visas. So we misunderstood the requirement. So now we have to initiate the request for the federal one and have it ready once we get a new ITA.
Regarding the NOC code, when I completed my previous Express Entry application I just put one position under that specific employer (last position held) and selected the corresponding NOC code. The reference letter that I got from that previous employer rightfully listed all the positions that I had held with them. When CIC rejects your application for incomplete information they don't necessarily go through all your documents. So now that I am reapplying I am double checking not just what was rejected, but everything. Hope this makes it a little clearer.