Hi,
You can think of the wave from each sub as having peaks and valleys (actually, they're compression waves, but for understanding what's going on, peaks and valleys work better). Now with different subs in different locations playing the same signal, the peaks and valleys arrive at different times and the offset can cause the peak to fill in the valley reducing the sound level and muddying it a bit.
This is the phase control issue and while for engineering math reasons is measured in degrees, what it actually does is advance and retard the timing of the peaks and valleys so that they will all arrive at your ears at about the same time. The easiest way to set it is to have some sort of constant bass signal playing and have someone adjusting the phase control until the bass signal is loudest. The means the minimum of peaks filling in the valleys and the best match for phase.
In terms of the cross over, I've always heard that you want about an octave overlap, so if your speakers are pretty flat to say... 40 hz, then set the crossover to 80 on the sub you're trying to match. Obviously, it costs you nothing to experiment so these are just starting suggestions. What sounds best to you is what is best for you.
Hope this helps.