The volume setting at half way is fine - that's the typical starting place for sub calibration. If you found yourself applying significant adjustment in the 990's menu, you might think about adjusting up or down. Setting the volume too high at the sub won't necessarily hurt it, but it could lead you to set a significant negative channel trim - this can lead to a subwoofer signal that is too weak to trip the sub's auto sensing trigger, leaving the sub turned off when you want to be using it.

The typical approach to setting the phase control is to play a test tone and toggle between the two. Whichever position produces the loudest sound is where you leave it. The 990's manual test tone can be used for this purpose.

I'd recommend setting the Cross Over to "Out" (which bypasses the sub's crossover). This is because the 990 is already providing bass management, and applying a second crossover (especially at 90Hz, where it lands very close to the crossovers you are likely to select in the 990) gives you two crossovers both operating in the same range. At best, this causes a dip in frequency response as the two crossover slopes combine. At worst, having a lower crossover at the sub than at the 990 will actually create a small hole in frequency response.