I tried placing my two F113s at the front of the room in the same plane as my LS360s with the sub/speakers crossed over at 80hz with my MX119. This did not work well due to my room accoustics - the main issue is that I had a gigantic spike in bass at 25-30hz that I could not eliminate even with the ELF trim on the subs turned all the way down to -12db. I also had a dip in bass at 60hz that is probably a room related issue as well as I have been able to minimize it with fine tuning of speaker placement and listening position but I have not been able to eliminate it.
I then placed my subs behind my listening position more in the back 1/3 of the room along the side walls and I am getting a very nice, much more flat 20-80hz response now from my subs. I used the polarity and phase settings to dial in the subs with the mains while running test tones around the crossover point with the mains out of phase and finding the lowest volume of the tone. They now sound perfectly blended in and the sound has a very even response.
So to answer the question I think having the sub in the same plane with the mains is ideal if you can get even frequency response doing it that way, but otherwise I believe it is better to find the location in the room where you can have the best overall frequency response and use the polarity and phase controls from there.
McIntosh MC501s, LS360s, XR27, WS350s; Denon AVR-A100; JL Audio F113s
ModWright Oppo BDP-105 w/Signature Truth Tube Modifications
Bolder Cables modified Squeezebox Touch; Denon DP-62L w/Ortofon 2M Black
ASC & RealTraps Panels; APS PurePower 2000; LAT International Cables
EVALUATION: ModWright LS-100 Preamplifier w/Phono Preamp Module