I think it depends on the type of game you're creating as to whether or not you think having a main event sheet is going to cause clutter. This is where creating groups becomes very useful; gets rid of all that clutter by grouping together related events.
I think you may be getting layers a bit confused there, though. You don't need a layer for every level. Layers are for seperating types of objects on your layouts; sprites on one layer, background on another, text on another, etc. You wouldn't store seperate game levels on them. That's what layouts are for.
You can have multiple layouts share a single event sheet, or each have its own event sheet, or each have its own event sheet, and include other event sheets.
You can set each layout to a single event sheet if you want, or have every layout have its own event sheet.
A better way to do it, personally, would be to store all your main game events in a single event sheet, but then have a seperate event sheet for each level to do all the things that are going to change per level. To include your "main" event sheet in every layout, you can use "Include event sheet" in each level event sheet.
If, however, all that's going to change each level is where you place your objects, then there's no reason that you couldn't do it all via a single event sheet.
I, personally, would start with one event sheet, until my project got large enough that I could see that there were some events that rarely or never changed (these would become part of my main event sheet), and other events that were being repeated, or changed for each level. These would become my event sheets for each new level.
If you're finding yourself changing the same variables over and over again each level, then that'd be a good reason to have one main event sheet, seperate event sheets for every level (aka layout), and include your main event sheet on every level event sheet.