The difference between the frequency which is sent to the sub because of the crossover setting and the frequency which is subject to the Audyssey equalization should be kept in mind. For example, if a "small" speaker has its crossover which was set at 120Hz during auto-calibration manually changed to 80Hz, the frequencies from 80Hz to 120Hz aren't lost, but stay with the speaker rather than being sent to the sub. The separate factor of the Audyssey equalization couldn't operate below 120Hz for that speaker because Audyssey only equalized it down to 120Hz(and manually changing it to 80Hz doesn't add equalization down to that frequency). This lack of equalization for those frequencies may or may not have any audible effect.

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Enjoy the music, not the equipment.