For phase, the rule of thumb is usually to play a test tone and try each setting - the one that seems loudest is the one to use.

For the low pass filter, I'd either disable it or set it as high as possible - the 990 is providing you with bass management already, so you don't need a second crossover getting in the way. With the 40Hz setting (assuming for a moment that you don't have all of your crossovers in the 990 set to 40Hz as well), you are throwing away subwoofer signal - probably a lot of it. If there's a way to disable the crossover, use it. If there isn't (and with a max setting of 70Hz I really hope there is), set it as high as possible.

The level should be fine at 5. That's where I tend to start, and then fine-tune the sub trim in the processor's settings.

The 25Hz level sounds like an EQ at 25Hz. I'd probably leave it at 0 like you are.