I stage manage with a community theatre. For my first two shows, I was a "co-stage manager". At first, I wasn't quite sure if it was possible, but my fellow stage manager and I turned into an amazing duo.
I feel like the trick is working the others strengths. I, personal, am more of a "people person", and better at communicating, while my partner has amazingly clever ideas, and is dreadfully organized. We basically split our duties. And when it comes to rehearsing, there was a good majority of the time where I was in the house, taking notes, next to the director, and he was in the booth, taking notes. We both wrote up rehearsal logs, and had separate "prompt scripts" but take time after each rehearsal to compile our information. We have a general rule of not addressing any major issues without the other, and to keep each other filled in.
I feel like it'll seem awkward at first, but if you're both willing, you'll eventually find a system that works perfectly. I'm currently working on several shows without my partner, and HATING IT!
Good luck, I hope that was helpful!