I've never understood that either, but I just ran them separate to be safe :P
I resorted to running mine under my car and back into the trunk through that pressure flap in the trunk, then sealing it with expanding foam... 1/0 gauge is damn annoying to hide in a car.
Anyone know what that flap is really for? I've heard it's to relieve pressure when slamming doors, didn't notice any difference there. Then I've heard it's so air can escape so the vents work properly... again, no difference. And finally I've also heard it's to let fumes and such out if you keep gas or something similar in your trunk, but I don't do that for fear of wrecking my Fi Q's D: