I'm not sure about phase, but the EQ setting looks like it increases gain. That is possibly for when different sized speakers are used; from small bookshelf to floor standing speakers; I'm not sure though.
The crossover should be set higher than the speakers lowest frequency capability. Looking at the NS3 specs; they are rated as 60Hz, so the crossover on the sub should probably be somewhere around 70-80Hz. You can adjust it a little to see what sounds best. You certainly don't want it set at 60Hz or lower, because the speakers likely won't reach as low as 60Hz and setting it any lower, would leave a noticeable gap between the speaker's lowest bass and the sub.