Sub Woofer Phase ?

If I am using my pre-out to connect to my sub and the pre-out inverts phase how do I insure correct phase with my main speakers ? I am using a CJ CAV 50 integrated and the pre-out inverts phase but the amp section does not. I am using a Martin Logan Depth sub.
Are you saying that the output from the pre-amp outs is inverted in phase, but the output from the amplifier is not inverted? If so, that means the preamp section inverts phase and so does the amplifier section.

If this is the case, we want to invert the phase of the subwoofer as well.

I think the Depth has a phase control that can be set at 180 degrees. Using this setting would theoretically put the sub back "in phase" with the main speakers.

The fact is due to recording issues, "phase" (especially bass) is all over the place in CDs or records. I constantly get up to correct it for various CDs or even songs within a CD.
i have started using the TruRTA program along with some pink noise to adjust the phase of the subwoofer to properly mate with my main speakers. it is amazing how little adjustments in crossover and phase will flatten out the in room response of your system.

Can you please talk more about the TruRTA program? Where Can I find more info on it?

I use Room EQ Wizard now.