For that open window deal, you need a proximity sensor. That will make it so the car goes off should someone try and pop your hood if the window is open. You may want to look into glass break sensors too.
That was a pretty expensive install for a shitty job. I knew you weren't gonna get your money back, but hopefully you didn't talk yourself out of a fix. I would not touch anything. They will say you fuked it up if you do.