First, the best way to set up your control surfaces is this. Set your transmitter travel for your surfaces to the maximum minus about 10. So if you can get to 150, set it to 140. Next, use your mechanical adjustments to get your surfaces to their high-rate positions as best you can. They should be VERY close mechanically. After you have done this then you can start using the Eq6 adjustments to fine tune things. Moving the center will affect the endpoints but adjusting the endpoints should not affect the center if you have calibrated the unit. If you have not calibrated the unit and you are putting in a a lot of adjustment though the Eq6 (which you should not be doing if you did things the way I mentioned at the beginning) then it will affect the center. If you do not setup your plane mechanically correct first and try to do it all electronically it will never be right. There is no shortcut here to do it correctly. Sorry if you knew all this but most of the people I talk to do not.
I don't know what I am doing wrong. For example: left elevator. I can set the center on both servos, I set the end point for one direction on one of the servos. When I set the opposite end point then the center changes. I use a template with 90 degrees 45 & 50degrees marked on it that lines up on the edge of the servo case and has a peep sight to line up with the bolt hole on the servo arm. If I set it at 50 degrees one direction and have to move it say an 1/8 inch on the other direction to get it to the 50 degree mark it will change the center by 1/8 in. Is this a calibration issue? Sorry to be a pain.