Suffice it to say that you'll have to be a tenacious bastard if you're determined to edit the prologue. I assume you mean the SNES version (I don't know much of anything about the GBA version). Essentially, the game doesn't have a script system or anything fancy to control the prologue. You'll have to edit code, or come up with your own scripting system and somehow manage to get that to work. Anyway you look at it, it will be difficult to do, and it's no surprise that Hyrule Magic doesn't let you edit it.