[bikeandestroyx]

To change what folder icons are placed in, you need to locate the app.dat (VK) or the initflashfiles.txt (Old Style). (See attached OEM and EXT for an example) In it you will find a line like this:
Directory("\Windows\Start Menu\Programs"):-File("App Link.lnk","\Windows\Original App link.lnk")
If you wanted to move This program link, to a subdirectory of your start menu, you would add the subdirectory folder name after programs.

For ex. move to system tools folder in your start menu.
Directory("\Windows\Start Menu\Programs\System Tools"):-File("App Link.lnk","\Windows\Original App link.lnk")
Also make sure the path is \Windows\Start Menu\Programs\System Tools, if you ehave it as \Windows\Start Menu\System Tools, it will create a duplicate folder In your start menu.

You can also rename links in the start menu this way, you just need to change "App Link.lnk" to "New Name.lnk". Do not touch the "\Windows\Original App link.lnk", that is just there to point to the original link location.