Yes, common issue. In my space shooter prototype in my sig I wanted the store to be an invisible/visible layer, not separate layout so I ran into the same issue.
The way I got around it was to use groups. If you own the personal edition you can put each layers events into their own group (right click event sheet and select "create group", nest events under it). You can then activate/deactivate the group anytime you change menus and they will be turned off/on.
If you don't own personal... you might be able to use variables to turn them off and on, but it would be very event costly.
thanks for the feed back! Yes Actually I figured it out later when I posted here! I also did the groups and activate and deactivating them fix the issue! But Still I have a strange bug! I have my groups likes
Main Menu (active on start)
Help Menu, under help i have for different options!
Option 1 menu
Option 2 menu
If i move my help menu group on top of Main Menu group! it works properly and fixed the overlapping issue! but if the groups are like I wrote above! it causes that very same over lapping issue! well its fixed just by moving the help menu group on top on all!