I am trying to take off my passenger door sill to run some wire underneath it and god damn. It feels like it will break before it actually just comes off. I don't want to have to replace this piece, so is there some special trick to getting it off? I only found one screw, so I am guessing it uses some kind of clips or something to hold on.

Yep, all clips. Use a one of those screwdriver looking thigs with a forked end to pry each clip up.