Set the frequency control to its maximum setting - the filtering in your receiver is setting the roll-off to the sub, and this control will have no effect unless you set it to a lower frequency than the receiver determines, which would be A Bad Thing.
Phase? Well, this determines whether the bass from the sub is in phase with the main speakers or opposite phase - ie the driver in the sub pushing out when the main speakers' drivers or pushing, or sucking when the main speaker drivers are blowing.
The setting is a matter of taste - I'd try it with the phase control set to 0 and see how it sounds, and then at 180 and see whether that gives better bass to your ears.