If they've got a jumper that can be used between two sets of binding posts I'd probably not put the woofers on the sub output - while it is a curious idea, you'll be using left/right separation (the woofers will share the same mono signal). I'd cross the fronts over at 40Hz or 60Hz (you can experiment with both and find the one your room and your ears prefer).

If you had the Yamaha for ten years, then it had at best a very rudimentary form of bass management - in fact, I wouldn't be surprised if you didn't even have a powered sub in the mix with the Yamaha, which would mean that there was effectively no bass management happening. That means you're entering entirely new territory with the 990's bass management. It also raises a question: do you have a subwoofer in the mix?