ASP.Net User Control Best Practice

My previous post about invalid cast exceptions turned out to be inaccurate.  Unfortunately, it was more in depth than that.  I am working on a project that has 37 user controls.  Until today, those controls were dispersed throughout the project in different sub folders.  This apparently is a bad practice.  If you have controls in two separate folders and Control A in folder Z references Control B in folder Y; and then you have Control C in folder Y referencing Control D in folder Z, that creates a circular reference.  This is because each folder in a website compiles into a separate assembly.  Assemblies cannot have circular references. 

Here's an article explaining it a bit more.  Moral of the story, put all your controls in a single directory or take the painstaking effort to be sure references don't exist in two directions.