1) Connect your 2-channel preamp to the unbalanced inputs and your pre-pro to the Balanced Input(s). Just don't play them at the same time.
2) Run ARO
3) Adjust the Fathom for your 2-channel system (Crossover, phase, polarity, ELF and Level).
4) Now, defeat the Fathom's crossover, leaving all the other 2-channel settings in place, and adjust your pre-pro for Multi-channel listening (subwoofer level, bass management, delay, crossover freq., phase, etc.)
5) To operate the system in 2-channel mode, simply switch the Fathom's crossover on... to operate for multi-channel turn the crossover off.
Note: If you use an active outboard crossover for the 2-channel setup (instead of the Fathom's crossover), you can leave the Fathom's LP filter switch "off" and avoid switching altogether and you also gain high-pass filtering for your mains. I would strongly recommend this approach.
Hope that helps,
JL Audio, Inc.