There's nothing like a fat-ass bass to mess your mixing , is it ? :D
Those guys swallow all freqs near (and not so near) them. There's 2 easy ways around this issue, both of them involve amp sims. The more popular way it's to record your bass in full tone , then thin it out using the amp sim's equalizer. The not so popular but often more effective way it's to cut most of your bass's lows before recording using your tone knob and/or sticking to the bridge pickup ; Once recorded, you can fluff it using the amp sim.