How would a MASSIVE conflict best be represented? I'm talking on the scale of two rank 7 or 8 rogue traders (more or less the equivilent of Lady Chorda or Calligos Winterscale) going head to head with the wealth of a whole subsectore at their dispossal.

Imagine fleets consisting fo dozens of ship ferrying millions of mercenaries or house troops across lightyears of void with multiple starsystems as the front line. I'm hoping my player play long enough to get to that point and I want to think of a good system for such a war.

Twilight Imperium, maybe? Or if you want something that needs less work 40kifying it, there's a "megacampaign" ruleset floating around 't'internets which mashes 40k (3ed), Epic 40k, Necromunda and Battlefleet Gothic for that sort of thing (ok, three of those games have had new editions since it was created, but it should still work).

For that matter, the map-based campaign system for Battlefleet Gothic should work reasonably well, seguing into the mass combat rules from Battlefleet Koronus once you begin a planetary assault.

depending on how the actual battle goes, you could use the siege rules from Frozen Reaches on a much larger scale, substituting city sectors with continents, planets, even whole systems