I just matched the bottom to top servos centering position and then match the end points, Some guys might program all 4 servos, I left the Default (in the master lets say) and matched to it

The procedure I used is like this,
Mount the servos in the wings, pick which top or bottom you want to be the "Master", with your radio make sure the subtrim is at zero deflection and the ATV at 100% (note it is important the sub trim for the chn and the ATV stay at zero/100% during the set up,, you can dial it back later, so if you need to move you linkage in to reduce throw to stop binding do it and max it out later) Make sure your dual rates are at 100% too. If the TX is telling the Mater to do more/less than 100% you're never get a match.

Adjust the Master servo with the flying trim button to get it centered to 90 degree. adjust the linkage to get the aileron set at center. Now with the Slave servo connected to the programer use the center function to center the servo, adjust it's linkage to center the Ail. Then with your radio move the Master to full throw and use the programmer to set the end points of the slave. Now once those inputs are matched what ever you do, subtrim, atv adjustment, expo etc. the servo should run together.

When you go to the other wing, don't worry about the first wing's trim changing from center, you can adjust the Subtrim with the TX once you're done programming.

Basically the same procedure for the Elevators

Also, I found programming endpoints just about impossible without using the computer interface,, using the programmer without the Computer for anything other than reversing and maybe servo speed is useless.

Good Luck