I am glad to see this post. I have a Yamaha 1600 with YPAO. I used the YPAO to set up and then went to the on-screen display and used the manual set up to tweek it in. However, as stated above, the manual is very confusing and I am not sure what I am doing. I have it sounding good but I am sure there is more I can do. I am not familiar with the 2500 but I assume it has on screen display.
Sorry I am not much help, but don't feel alone. I look forward to any feed back on this issue. I have had my Yamaha for a year and feel I don't understand much of it. I jumped from two channel stereo from the early 80's to this amp with 7.1 and feel lost. Love the sound but I know I am not using it to its full potential.