Can't speak for the E-6, but on the EP-3, you start out as a Navigator for about a year, then move up to what amounts to assisting the Senior Evaluator, who is also an NFO, and who is responsible for collecting/fusing/reporting the information collected by the aircraft and its operators. After a year of that, you move up (qualify) from assisting to being the SEVAL. Basically, you run the reconnaissance mission. If I get any more specific than that, I'm going to stray into classification issues.
It's somewhat similar for the Orion. Start out as a Nav, then wind up as the guy running the mission. The navigator portion for these platforms is actually the minority of what the NFO does. The majority of time is spent qualifying for, and then running, the actual missions.