It's been a long time since I last used game maker but normally regardless of your engine there are two ways to do upgrades.  Fist method is to have your upgrade button trigger a flag/Boolean variable that tells a script to change the method/class/function/code used to change the score via an if statement. ex:   If {upgrade1==true} score = (score + (scoreup*2)) 

else score =+ score

the other way is to have an extra value in your score changing code that starts at 1 or 0 ex: score = score*scoremultiplyer

and then increase scoremultiplyer when upgrade is triggered.  If your engine supports it I suggest the latter as it is slightly faster and often easier to maintain.  Sorry I can't be of more initial help but I am recovering from a stroke and I don't remember much about your engine. if you are ok with switching engine there is a wealth of tutorials for Godot 3.5 and GDevelop and they are both free. I Have managed to make working clicker alphas on Godot 3.5 and Godot4 beta pretty easily since the stroke, so I suspect they are quick and easy to learn.