Tuning down puts your bass in A0, which is around 28Hz - the G below that is like 24Hz or something. You're so close to the bottom of the human hearing range that it gets hard to actually distinguish the fundamentals, because they literally are just rumble - they're well into the sub-bass range. As soon as you EQ the bass, you'll probably cut most of that out anyway, which makes the entire exercise fairly pointless.
You'd be better off playing the bass line an octave up (the same octave as the guitars). You'll still get plenty of low-end rumble from the bass, and it'll sound like a bass (rather than a guitar) because of the p'ups, the string gauge, etc., but it'll be clear enough to hear properly. That's how Meshuggah work with the 8-strings - the guitars and bass are in the same octave. Think about it; why do you need a bass under a guitar line as low as most bass lines anyway? 9 times out of 10 it's nothing more than adding a layer of woooooompf to your track.
Steve