If the speakers are set to large, the crossover does not get applied (full range goes to the speaker, nothing goes to the sub). There's only one exception: if the fronts are set to large, you can set the sub to "L/R+Sub" and you'll get "double bass" - the mains get full range, but the sub also gets a copy of everything below the fronts' crossover point. I've got a detailed run-down of the 990's bass management here in addition to the notes in my main review .

If your front speakers don't go below 40Hz, you're probably best off setting them to "small" so the sub can handle the material below the crossover point.