Phase you have to play with - set it where you think it sounds best - this will depend on where your speakers are relative to each other, where they are in the room, where you're sitting,etc. You might not notice much difference.

For crossover - well, if I knew your receiver was cutting the bass to the speakers I'd say turn it up as high as it goes, but since I don't I'd advise you to cross them over wherever the HTIB manual suggests.