Hey
Mya :wave: I'm glad to see you've gotten things home and up and running! Lets see if I can help shed some light on a few subjects, and maybe offer a few tips along the way.
Firstly, I would strongly suggest that you actually read through the user manual and suggested settings very carefully (boring, I know). Your new Denon AVR-4311 is an advanced piece of kit, and most importantly the calibration function Audyssey MultEQ XT32 demand extra attention. Visit Audyssey's website where you will be able to read lots of tips and guidelines that can be extremely helpful. Here is a direct-link just to get you started (you can also submit your own questions):
http://www.audyssey.com/audio-technology/multeq/how-to
To ideally place speakers in a listeningarea is no easy task. Like many of us you might find that over time you'll keep on experimenting with placement to obtain improved results. And as with most speakers Apex will reward you with carefull placement. Also remember to run Audyssey calibration several times to learn how it works. Something I strongly suggest doing. Especially after the Apex have been fully run-in and/or whenever you change things around in your room. Most changes will affect the sound, and Audyssey will take those changes into account when calculating the results.
Now on to your specific questions:
1) automated distance measurement of subwoofers can often times turn out incorrect (the issue is addressed in your Denon manual, and on Audysseys website). This can be caused by the layout of your room and how low-frequencies are picked-up by the microphone. Simply change the distance of the subwoofer manually in the menus on the Denon to its correct distance (after the automated calibration procedure). Alternatively, you may actually want to play around a bit with the distance to determine by ear which sounds best to you.
VERY IMPORTANT: turn 'Low Pass Filter' to OFF on the AW-12 subwoofer. Audyssey will set internal filters according to the calibration and so this task should only be handled by the receiver, not the subwoofer (otherwise you will use double filtering). The frequency knob on the subwoofer then becomes obsolete. When running the calibration the determined frequency cut-off will depend greatly on how the Apex satellites perform in your room. During playback if you happen to find the cut-off too high or too low simply change it manually to your own preferences (80Hz is always a good starting point). Volume, Phase and EQ1/2 are a matter of interplay with the satellites and personal taste, I'd say. Try find a smooth balance.
2) dont be present anywhere inside the listening area during the automated calibration! And definitely NOT beside the microphone, as this will disrupt measurements! Take great care when placing the microphone and definitely use a steady tripod when doing so, as suggested in the manual (improves measurement accuracy). Make sure you angle it toward the ceiling, placed at the same height as where your ears would be when normally seated. It is essential you run all
8 suggested measuring-points around the listening area as this will allow Audyssey to collect as much acoustic 'information' about your room as possible and the character of your speakers in order to accomplish maximum result (better sound). Follow Denon and Audysseys recommendations on microphone placement within the listening area and try your best not to stray from them.
3) again; placement is often key in creating a realistic envelopment of sound, but every room and situation have limitations so compromise is often difficult to avoid. My own pair of A10 rears are placed behind the listeningspot on each side of the sofa, about 1.5 meter away, angled slightly toward the listeningspot. This workes great in my room, and offer a more 'direct' surround. Your situation might be different though, so again: Experiment! (and then re-calibrate Audyssey!)
Yes, all of the above may sound time-consuming. But its fun and rewarding, believe me! So enjoy the Apex and the thrill-ride they are capable of. You only just scratched the surface. Good luck!