Currently, when I change layout, the global variables will reset
Unless you are triggering the "Reset global variables" action, they shouldn't be. That's the whole purpose of global variables.
Global Variable Demo Capx
R115: Press space bar to progress to the next level. Notice how the score does not reset.
Be sure you don't have any "On start of layout" events where you are setting the score back to 0 - this will fire every time you change to a new layout, not just the first time you start your game.