|There's more than one way to do things|
I have no experience in this matter so mine is an idea more than a suggestion. Hope it's appreciated and gives maybe reason to meditate or find a better solution.
Can you maybe develop what you need in a module, separated from the original code? It would give you the basis to "don't fix if it is not broken" and would allow you to do "occasional changes" to the original code, "to fit your necessities for the new functionalities".
I believe this could be some kind of workaround to facing your boss directly on how he coded and how the code makes your life difficult, but if you proceed wisely, you could just obtain what you expect, I suppose.
Hope it helps :)
update: extremely important
Backup. Backup everything before typing a single character.
Don't even think about modifying something you have not backed-up! If something goes wrong, be personally assured that a quick replace can bring everything in working order!