Welcome tomtuttle, thought I'd add my experience so far as a fellow newbie. At first I was also very concerned with mains integration, but soon realised as you have that small changes in sub location can make big changes in response.
So, what I did first was find the sub location that gave the smoothest response that followed the "ideal" target curve, then adjusted my seating location to reduce dips/peaks. After completing all the sub measurements, I discovered that the mains by themselves, had a dip in the crossover region which I corrected by repositioning them for flatest bass response. A few tweaks of the phase control and the full frequency response looks as flat as ever.
My point is it may take allot of measurements but once you see how the location of your sub, your seat and your mains interact, you will be on your way to smooth listening
Have fun.