With the 990 already applying a crossover, the sub's crossover becomes somewhat unnecessary (it is intended to deal with a full-range input signal, not an already low-passed signal). I would recommend setting the sub's crossover as high as possible - all the way up to 150Hz. This will keep the sub's crossover from interfering.

I have Paradigm Studio/60's, which I crossed over at 60Hz for a long time. I recently changed my crossover to 80Hz, but that was due to a separate issue (my SMS-1 revealed a room null at around 63Hz, which I could correct by moving the crossover up to 80Hz and equalizing the sub's signal around the null).