if one of your speakers is "pushing" air (cone extending) as another is "pulling" (ie cone retracting), they can in certain conditions cancel each other out, or have a host of other problems. sometimes having things 180 degrees out of phase (the equivalent of having the wires ("polarity", but term used loosely) reversed) can help matters, i've seen people do this with rear-facing subs, i also do it with my dash speakers - they fire at the windshield, and the sound bouncing off the windshield actually sounds better when they're reversed.
i'm pretty sure having them on the same plane means that the sub would be pushing air into the main listening "chamber" (ie, the cabin) on cone extension at the same time the other speakers would be. if your sub is in your trunk, this is unlikely to be true. with a sub though, it's really a trial and error thing - i for one know i'm not smart enough to mathematically figure out the phase of subwoofers (the wavelengths at sub-bass frequencies are massive) so whenever i'm putting one in i experiment with the phase and see what sounds best.
hope that long winded post helps.