There isn't really a way to be 100% sure someone isn't cheating. Splicing, audio, visuals, hardware mods, scripting, etc. These things, depending on game, can be done with no way for the viewer to know if it's cheated or not. Most leaderboards operate on video proof and trust. If that video proof can't be determined to have been cheated, then it has to be taken as legitimate. The only way you can discredit legitimate looking proof is if the runner outs themselves as a cheater.

Having said that it still depends on the game/board. Some games even allow external hardware/software. I know years ago there was debate over using some adapter to make ESS easier in OoT. Something to do with joystick deadzones. Not sure what the outcome was, but the point is that hardware modification might not even be seen as cheating depending on the community.

It's a setting in the timer software. I forgot what it is called, but just go to the preferences of LiveSplit, and there's a way to force it to stay on top of everything else.