Audyssey most likely set it at 100Hz becuase your main speakers were not responding that low. And yes, you will miss out on the range of 60-100Hz by having both crossovers set that way. If I were you, I would turn the crossover knob on your sub all the way up (most likely 120Hz). By doing so, the crossover on your sub will be bypassed and the crossover in the Onkyo will be the only one active. I think 100Hz is a little high, but without knowing your equipment and setup, I would say that it would be best to just use the crossover in the Onkyo.
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