I think either a composit map or two sets of maps is probably the only way to resolve the issue. The problem is that the individual systems are probably in the range of 18 to 20 AUs in diameter. On Ara's map, the planets beyond 2 AUs from each star are orbiting in adjacent hexes.
Take our solar system for example. The Sun, Mercury, Venus, Earth, and Mars are all in the same hex (roughly 0 to 1.2 AU). The Asteroid Belt (roughly 2.4 AUs) and Jupiter (roughly 4.8 AUs) would be in the next ring of 6 hex. Saturn (aproximately 9.5 AUs) would be in the next ring or hexes out. Saturn's orbit probably about the limit for any of orbits on the Firefly verse.
So, you can use Ara's map to show the relative locations of the systems, and then you probably still need a second map for each system that shows where the planets are in their orbits.
You could use the jump 6 map using a 1/2 AU scale for the center hex and the first 3 rings of hexes, then a 2 AU scale for the next 2 rings, and 4 AUs for the last ring, and it would all "fit" into Ara's map scale of 4 AUs per hex.
Of course, then you are back to the issue of tracking the location of the individual planets. Which is why Celestia is such a nice tool for this, because it does all that work for you. So, you use Ara's very nice map for general reference, and then use Celestia to show the actual positions of the planets and the actual distances from point of departure to point of destination.