With my system, the TA is done by inputing the distance from each speaker to the listeners ear. After I did that, I used a test disc with mono center channel recording and adjusted the settings by ear to get it as close to center as possible. I also had a test disc that had tracks that would isolate the tweeters and mids so you could do the adjustment for each without influence from the other driver.
TA will not be able to overcome all your problems though. Since I'm using stock speaker locations I could not get a perfectly centered image. I just settled for as close to center as I could get it with a decent sound stage height.