Problem with a custom plugins

I have several plugins and many of them do I edit the source code to customize based on my needs.

However, every I update the plugins, I must make the edits again.

I can create a function, so that even when upgrading the plugin, the changes in functions that I realized, don’t changed?

And recently, also had the same problem editing function “start_el” of the file wp-include/classes.php, because when you updated the wordpress, the class of the “active” for menu, back to the default.