Hi Frank,
Congrats on the Fathoms, I think you will be very happy. Since you have Audyssey (Multi EQ?) I would recommend running the Fathoms as master/slave and run ARO from the master sub before running Audyssey. Set the Master Fathom in Ref mode which turns the level and phase setting over to your AVR/SSP and Audyssey.
If you are not happy with those results, you can run the Fathoms as dual Masters and use the Variable instead of Ref setting to play with Phase and Level on each sub. Dual master mode will require you to run ARO separately on each sub. Once you get to the best sound out of that process you can use Audyssey to smooth the overall response.
It is really a simple but time consuming process. I hope you enjoy your Fathoms as much as I do mine.
