Will the screen go bad if I use this LCD tweak for a longer time? And how to prevent anything bad that might happen to my P's if I use the red color on my LCD?
It's an LCD screen, so burn-in will (likely) not happen.
It's software based.
There isn't really anything you need to do to prevent something bad happening; as usually you can just reset your P's, download it and then it'll be fine.