Start by preparing the icon you want to use for your stack overlay.  Extract the icon from your download and put it in the folder you want to make a stack.  If it comes in an icontainer file you can load it up in CandyBar and then right-click it to extract it to an ICNS file.  Next you need to name your stack properly to make sure it always appears first which is critical to the overlay effect working properly.  I like to either give my stacks a blank name or begin and end my stack icon names with a dash “-” character because I like my stacks sorted alphabetically by name and the dash is always put before “A” and “1″.  Next you can change the file attributes to hide the extension and you’l have nice looking stacks that show up as “-STACK-” in grid, list and fan views.  Now just drag the folder with the properly prepared stack icon to your dock.  Once there, right-click the new stack and select the sorting and view of your choice.  Check out this visual tutorial that will step you through all of this.   I don’t recommend sorting by date because every time you add a new app or document you will have to make changes to keep the overlay icon on top.  You are now ready to enjoy your new Snow Leopard transparent stack icon.