1. By "folders window", do you mean a "folder portal"? 

2. It might be really helpful if you posted a screen shot of what you mean.

Hmmm

I've been using Fences 3. Is Folder Portals an addition to Fences 4 ?

You want a screenshot? Not much to show you. It's a folder. I want to organize the icons.

No go. It says "Files in a Folder Portal cannot be manually repositioned." I can change to certain orders but not reorganize them as I want. 

As I originally asked: is there way to (manually) organize icons in a folder window?

That answer does not quite make sense to me. The desktop is controlled by Windows also, but Fences gives a way to move organize and group icons. 

That is not quite correct. Yes, you can move them around but they quickly reposition themselves in the grid pattern. I can't place them the way I want, with some over here and some over there.

No such program that I am aware of currently exists.

For that to happen I believe you would want to find a file explorer alternative. Of the few that I know of  none function the way you are wanting them to.

With that said. The idea of Stardock making their own file explorer alternative actually would be kind of cool. Not a bad idea.