I was in a two-bass band a few years ago. It can work, but it takes some give and take. Here are some things we did to make it work for us:
1. Different tones. The other guy was old-school, using flats and a foam mute. I was all about bright and modern. The other guy was strictly a fingerstylist. While I also primarily played fingerstyle, on certain songs I would use slapping or a pick. And the other guy wasn't much of an effects guy, although he had a Sparkle Drive and a Boss Chorus. I had a board full of weird stuff.
2. Different roles. As you might imagine from what I described above, the other guy fulfilled the traditional bass role 75% of the time. I would often comp chords, play melodies, or solo.
3. Different registers. I used a 6er, which gave me a few extra notes both below and above what the other dude had. Someone's gotta hold down the bottom, but if you're both trying to do it, there's gonna be mud. One of you has to be willing to take the high road, so to speak.
4. Space. Sometimes to the point that one or the other of us would rest entirely for a whole section of a tune. But mostly we kind of danced around each other.
5. Having both bassists meet for writing sessions outside of practice. This allowed us to get parts happening that didn't step on each other's toes. At our best, we sounded like one huge bass part, an effect our drummer dubbed "the uberbass".
To me, the interesting part of the challenge was this: when you show up to play music as a bassist, you normally know exactly what role is expected of you. But how do you negotiate roles when there's two of you? Trying to answer that question proved to be an intriguing creative catalyst.