I would not touch the PEQ on the Rythmik if I were you unless you have a specific bump that you measured with a software and adequate mic.
It took me 6 months to dial in my 2 F12s and having Brian and Enrico scratching their heads on why I was not getting the expected performance from my subs. It wasn't until I started actually measuring the room and seeing the effects procured on the sound by moving speakers and subs that I was able to get the integration between mains and subs.
If you use your sub/s to listen to music and films, I would greatly recommend to go down a very unusual path: place a switch between your pre/amplifier and your sub/s and connect the LFE and LINE IN on your sub to the switch. In certain circumstances like mine the settings and eq you can achieve with your preamp do not allow you to get the best of both worlds. So going for a more analogical approach to set the integration between subs and mains will yeld the best effect, while for film and concerts, since there is an LFE channel, you take full advantage of the way the source is encoded.
First thing you'll need to do is to check that your mains are actually in the best possible position and are performing to their max. In my case I had to move them closer to the back wall and closer together to diminish a suckout between 50 and 60 Hz. Trying to compensate the suck out by crossing over the subs at 50 or 60 or even 80 did not help. Moreover, if you do not have the paper cone version of the F12, I can assure you the F12 produces a quite bumped up sound around that frequency, so crossover should not be higher than 60 Hz possibly even lower. The effect of repositioning the speakers was to move the suckout more up in the audio spectrum (between 70 and 80 Hz), but at a lesser degree.
I run my speakers full range, although Yamaha has a starnge way of handling this when adding subs. The setting called extra bass, in presence of a sub, creates a roll off curve at 40 Hz, which happens to be the lower limit at which my ProAc speakers play without loss.
After finally getting a very good imaging and bass from the mains, I placed the subs in the corners behind the mains and pointing allong the walls. Took a measurement from 20 to 500 Hz with my main speakers off.
Then started taking several measurements placing the subs in various positions and angles.
I ended up with both subs out of the corner by 15/20 cm and facing the opposite corners of the room for the smoothest response.
Throught the meaurements I was also able to see that the Yamaha behaved in a very strange way when set to output bass from mains and subs. It cuts off the sub at around 35 Hz. Since the sub curve starts 12 dB higher than the lowest point of my mains (mains show around 70 dB at 40 Hz while sub is at 82 dB at 20 Hz) the crossover between mains and sub happens to coincide at 40 Hz.
I have also found that by setting the crossover on the subs at 80 Hz I could get a little more residual output above the 50 Hz point, which provides an even better integration between mains and subs and as an unespected side effect it ended up to reduce of a couple of dB the suckout on the higher frequency (between 70 and 80 Hz).
Last, but not least, using the LINE IN gives you full control on the phase issue. I used REW's built in frequency output and set it at 40 Hz, which is the crossover point. Both main speakers on and only one sub on. I measured the effect of changing phase on the sub with REW's db metre. Once I obtained the highest output I stopped the phase adjoustment. Then turned on the second sub and did the same.
Of course, before setting the phase, you should adjust the distance of your speakers in your preamp.
Since I have a Yamaha, I have the ability of having to setting patterns so I can have one only for stereo listening and one for the full atmos system. For the second I let Ypao do its thing and just set the switch so that LFE and bass managed sound (60 Hz) is directed to the F12's LFE input.
I was not able to get a good result for stereo listening usinf LFE, EQ, or anything for that matter.
Compared to my previous REL R528 I am getting a lot more articulation, better stereo separation and integration between mains and subs. What I am not getting is the massive bass I was getting with the REL's, which were overriding my mains. It may seem fun to hear Muse FOLLOW ME moving air in the room, but what you were actually missing was all the detail and lower end notes that the REL's could not even approach (roll off started at 25Hz and at 23 Hz they went silent or the passive woofer flapped).
For film I set the F12's at 14Hz extension (same as music) and LOW damping. I set the on/off switch to AUTO so the limiter is engaged and simply enjoy films and music with a whole lot more down there. And when in music mode only, I can assure you I am not able to discern if it is the subs that are giving me the great bass or my mains, which are pretty incredible. And detail, imaging, depth are out of this world as the room just simply shrinks and increases in size following the recording.
It was a very long process and after the first month with the F12s I was ready to sell them, because they were even worse than the RELs. Only thing I was appreciating was the lower end effects in films that were simply not there before (raw of the beast at the biging of Helloboy 2 just an example or its footsteps feeling his presence even before he is revealed
). But was I wrong!!!!!!
Don't give up and try les ortodox approaches, because every situation and need is different