This isn't that easy - if you have 3 versions of a program (version A, the original, and 2 forks - versions B and C) you cannot blindly take version A and apply all changes made to it in version B and then version C, as version C might delete some code that version B relies upon.
You will have to manually review all of the differences to see which ones will work together and can be merged. For this, SuperC is an excellent tool.
It sounds as though at your site you have now got 2 modified version of a program, both different, and you like to combine both of these into one single program. I'm afraid this cannot be automated and will have to be done manually.
It may be relatively straightforward if both versions of the program have made changes that are in different areas of the code, or tricky if the changes are in the same area, but even for a 'straightforward' case, it still needs manual checking to ensure that changes to not impact each other.