Unzipping an archive, the folder icon appears under the archive
You could change the "view" of the ~/Downloads folder to something other than "as icons" from the Finder menu "View". In "list" or "column" mode, they would not be on top of each other.

Alternatively, under the "View"->"Show View Options" you could set it to "Sort By" -> "Snap to Grid" and all new icons would be nicely arranged it a grid. Additionally "Arrange by" -> "Name" would put things in alphabetical order, and not all on top of each other.