I don't see any problem with tricking it a bit by taking energy out of a peak and then running the Audyssey. Then tweak with REW after. The usual fare seems to be that people run Audyssey first and then work with REW to change the low end, but whatever works.
I'm never thrilled about a 100Hz cross. I think it localizes the sub too much. In addition to phase adjustments to correct the dips around a crossover cause by interaction between the sub and mains, you can also alter time delay on the sub using your receiver trim for distance. This can be quite successful.
brucek