I don't know of a way to stop the script debugger and data viewer from sitting on top of all other windows. However, I use a program called Divvy to make window management easier. I know there are other tools that do similar things if you don't like how that one works.
I don't believe it can be restacked. It's intended use is to allow you to run the script and see what is going on as it runs, which is why it stays in front. However, you can customize FileMaker's status area by adding the Debugger icon to it so you turn it on and off with a single click at any time without having to use the Tools menu.