My thoughts about the correct use of GPS is that a plan should be made first, i.e. by drawing lines on the relevant chart/s. GPS should be subsequently used to make the route easier to fly. The GPS route should be checked against that plan. If there is any discrepancy, the flight must not go until it's resolved.
After all, it's by no means unknown for a "traditional" paper PLOG/flight plan to have errors on it, too, such as an incorrect track or distance written down, or a total time added up incorrectly.
One plan is used to cross check the other. I'm fortunate enough to have a moving map display, albeit a very basic one, which can usually be zoomed out to show the whole flight.. If the moving map track lines don't match the chart lines, that's an instant "stop" signal.
Once the route is in the GPS and checked, I often save it if required, for a later date. The "box" is subsequently highly unlikely to make an error in that plan.