Jose, definitely use YPAO. I'd suggest setting it to skip the speaker size and crossover frequency adjustments and instead manually setting those to the THX recommendation of all speakers "small" and a 80Hz crossover. Another point I've found is that it may give better results(although this might not apply to your listening room)to set the equalization to give preference in adjustments to the "low" area, rather than "flat", which tends to use its limited equalization assets over the entire frequency range equally.
