Thats a misconception. The sub's lpf is always in the circuit, and downstream of the line input, so it most certainly will work in conjunction with the receiver's sub out connection. The sub preout on that stereo receiver is either not filtered (full range signal) or might have a fixed lpf but at a higher frequency that you likely need, so you'll have to rely on the sub's lpf.
The phase swich has nothing to do with the plane of the speakers. It's there so you can better dial in the crossover between your mains and sub. I encourage you to try both settings of the phase switch and choose what works best.
If you're doing the calibration by ear, it will be a shot in the dark. If you have REW or Dayton Omnimic, you could dial it in more precisely.