If I understand correctly you have your game menu just on another layer but in the same layout as the actual game. Or did you confuse layers with layouts?
You really should use different layouts for menu and the game itself (at least if there's not a good reason for having them both in the same layout. I can't think of one right now). Just rightclick in the project tab and select 'Add layout'. You should have Layout 1 and Layout 2. You could name them now 'Menu' and 'Game'... well and that's that. And when you click on 'new game' now in the layout 'Menu', just add an event that goes to the layout 'Game'
A layout is one screen of your game. Think of layouts like pages of a book. You would have one for the titlescreen and menu. One for the game itself (which may have many more layouts for different levels). And probably other layouts for credits screen, hiscores, etc. Layouts can contain multiple layers.
Layers... think of these as tracing paper. They're useful for seperating your objects. For example, you could have a background layer (far away hills etc) and a foreground layer (some buildings). The foreground layer would sit on top of the background layer so you can see the background through any holes in the foreground. You could control these layers to scroll at different speeds giving the illusion of depth.
Since you're just beginning you only need to worry about 1 layer for now... and really... just one layout too.