Its important to realize that peaks can be attenuated using either Audyssey or the PEQ but you can NOT boost a null. A strong room reflection can compete with the direct signal source and if they meet up at your ear as crest-to-crest or trough-to-tough they will be additive and attenuation will work to lower the overall sound level at that frequency... however if they meet crest-to-tough they will tend to cancel (similar to how noise canceling headphones work) and boosting will cause equal increases to both crest and trough with the result being the same null. Keeping this in mind...
In general this is what you should be looking to do...
Pick a location for the sub that seems to eliminate or at least minimize any serious nulls from all the listening position(s). Then run Audyssey to attenuate any peaks and you will have the best in-room response possible. Its a relatively simple thing to do. I don't know what testing or monitoring equipment you have at your disposal or what you might be running for mains so to keep it really simple just download a sweep that covers the range from 10Hz-150Hz or there 'bouts and play it at approx. 75-80dBs over and over again as you sit in each of the various listening positions. You are listening for nulls, either full or partials... ignore any peaks you hear as they can be EQed out later. At a full null the sound will completely vanish, you cannot tolerate even a single full null... find another place for the sub. A partial null will cause the sound level to dip, if its not too bad don't worry about it as every position will have some dips, just find the sub position with the least and shallowest dip(s) and call it good. Hopefully you won't have to try more than 2 or 3 positions... most people with wives will find they only have 2 or 3 choices given to them anyway
If you wanted you could use PEQ to remove any obvious offending peak and then let Audyssey take care of the rest.
I personally don't think bass traps will help with smoothing freqs much below 80Hz... plus they can be very large while only resulting in a modest improvement. I use them myself but can't and don't rely on them to deal with room modes.
Bottomline... sub positioning and listening locations are what you should try using to eliminate any nulls.