When I open livesplit usual my splits are in front of everything, but when I open super meat boy they fall back and I can't see them when I'm playing, does anyone know how to fix this.

Livesplit can't go over your game in fulllscreen mode, if you're playing windowed however, to make livesplit always show on top of other windows :

Right click your splits on Livesplits, edit layout > layout settings > "always on top" checkbox bottom left