I realized this. I appreciate the help! Very much. But, is there a way to keep him hidden after the script? 'Cause whenever I exit the route, and come back in, he's right there again. I came up with, what would be looked at as fixing it with duct tape, by placing script tiles at the entrances that check for the flag that was set after battling him. If it was set, it would hide the sprite before I could get to him. Which is what I wanted, but I feel like that's a waste of memory.
Haha. Yeah. Used to be Advanced Trainer that wouldn't work(It would close out as soon as I clicked anything after I opened it). But, it works now, and it's now XSE occasionally messing up. Honestly, it's a bit annoying. I just hope the next tool to mess up isn't Advance Map. :P