You are not going to get a lot of guidance from the program in this regard and there is no actual "change form" in the program. The program will check the Amended return box on your 1120-S and K-1(s), however.
The best you can do is to enter the changes (after saving your original return under a different filename) and then use the Miscellaneous Statement form and enter line number (and Schedule, if necessary) along with the reason for the change and the amount.
