How can we edit a file when using Compare files? The differences show nicely; but, so what. I can't find a way to edit a file to fix the differences

Unfortunately you cannot edit whilst comparing and a simple editing feature would sometimes be nice.

There are many utilities that do support that, such as Beyond Compare from Scooter Software, UltraCompare from IDM and Araxis Merge. All of those also have many more features than can be reasonably expected in an IDE such as PhpED, so are well worth you reviewing if you do lots of comparison work.