I have done absolutely nothing to the engine to change it for the bosses, I'm not good at coding as I said so I've been focusing more on other things right now. I just want a boss good to run by z3, I'll send you the GMK file in a PM, but don't expect much from the simple dungeon I have whipped up, its something I made in about 10 minutes just to have something at least for now, the actual dungeon is almost complete on paper but I haven't really started it yet due to pure laziness.
But to answer your questions, no the bosses room will not be bigger then 160x144, I have the bosses sprites & spritesheet in, but haven't done much with it, and i basically just want ganon to teleport around and do a different attack each time, like a slash for one, fireballs for another, ect.
It actually doesn't sound too difficult, but my limited GML skills make it much more annoying then it should be.