I love to keep things organised, and with my current project closing in on 400 events (at this rate it'll push 1000 when completed), I have to.
For starters, I've put global variables into their own event sheet. I've also put all reusable game logic into its own sheet called Main Mechanisms. Then, every level/screen/etc has its own sheet, which is a very trim, very neat little thing that I can use to change level parameters quickly.
I use groups extensively - probably have about 40 at the moment. And sub-groups too. Basically, whenever an event looks like it's going to be larger than the height of my screen, I put it in a group, together with anything that would logically go with it. All my initialisation stuff is in its own place, so are my settings for mobile, my controls, AI, world events, etc.
Getting organised early and staying that way is good practice.