OK, first off I heard them Yamaha towers and they aren't bad at all {a little over priced but sound decent}. For the mic placement are you putting it at the middle seating position or in the middle of the room, it was my understanding it should be at the ear height of the center seated/listening position, mounted on something hard {not a bunch of stacked up pillows, I have seen this make a difference}. Everything should be quiet {no talking or phones ringing}...
I personally only use the auto setups as a starting point, it gets the phase and speakers all in the right position... But for the most part do the crossing and balancing myself... I use one of these for the balancing
Amazon.com : USB Handy Digital Sound Noise Level Meter Decibel Pressure Logger with Tripod Mounting : Digital Voice Recorders : Electronics , I start by getting them all in "phase" toggle through the phase settings and pick the loudest on, then just run the avr through its test tones for each speaker one by one and set them all to the same level, so you play center at 0 and look at the meter, if it is reading 90db at the listening position, now move onto the front right and set that to 90db, then front left set to 90db, and move on through the lineup..... that will balance everything out.. Now for crossing, I would set your front to 70 or 80hz high pass and set the sub to the same thing except low pass... that will get you close, you may need to play with the levels a bit after, some people like to run the sub hot and some like to run the center hot, I prefer the sub set back a little and the center a little louder....
Believe it or not your front left and right aren't going to do much and your surrounds are going to do much less, your center and sub in an HT do the lions share of the work... Now for music its an entirely different ball game, run your fronts direct stereo full range and they should sound best...
good luck... and welcome to AH
