What's happening is when you add to the layout size vertically, it's adding to the Y coordinate and that means it has to add downward. What you need to do is start the game by using "scroll to position" and set coordinates. Use on "Start of Layout". Then the game will NOT start in the upper top and left. For example, assuming your layout size is 3000, 3000:
System > On Start of Layout > System > Scroll to 1500, 1500
This will start the game in the middle of the layout.
Hope this helps