We use magnetic lights, but use them somewhat differently than most - I set them up INSIDE the towed vehicle, on the rear shelf right up against the rear window. Ran the wires for them down to the trunk, them from there up to the 6-round plug at front of the vehicle.
They pretty much stay there all the time. They sit right behind the rear headrests, completely out of the way and don't block your rear view, so no real need to ever take them out. They stick in place, using pieces of velcro I attached to bottom of the lights.
This is kind of the best of both worlds, for us - Permanent installation, nothing to have to put on or take off with the lights. Just plug up the 'umbilical' cord and they work. But, without having to tap into the vehicle's tail-lights at all. Very inexpensive, too, since magnetic light set can be picked up for just $20 or so, and can be used on your next vehicle when/if you ever trade.
Nice choice, BTW, on the Ford Flex. We seriously considered going that route, and may well replace the minivan one day with a Flex. The Flex is one of only a few (newer) vehicles I've seen that is flat towable from the factory and provides 3 rows of seating.
