Once I have shot and recorded the click values for 400,600,800 and 1000 yards, do I need to enter the click values for each of the ranges shot or just the 1000 yard click value into the truing feature of the program?

I think it depends on both the program you are using and the use you want to put the rifle to?

Also, the next time you go out it won't be the same.

Hopefully, you're not planning to shoot game at the most extreme ranges mentioned. Elmer Keith reported that many bullets could not even penetrate the ground at 1000 yards.