The scope of the search is relative to the element on which the method is called. Elements are returned in the order in which they were encountered in the tree.
When searching for top-level windows on the desktop, be sure to specify Children in scope, not Descendants. A search through the entire subtree of the desktop could iterate through thousands of items and lead to a stack overflow.
If your client application might try to find elements in its own user interface, you must make all UI Automation calls on a separate thread.