If you want to rearrange the placement of shortcuts on you start menu, it is as simple as cut and paste.
First we need to understand where the various sections that are displayed on the Start Menu come from.
Looking at the partial Start Menu image
we can see a number of sections. Let us call the sections on the left hand pane that contains ("Shutdown", "Run", ..., and "Programs"), "SYSTEM". The Section above this is "All Users/Start Menu" and the left, top most section is "Current User/Start Menu". The "All Users/Start Menu" shortcuts are located at:
%windir%\Profiles\All Users\Start Menu
To add an entry to your Start Menu here, simply paste a shortcut in this folder.
To add an entry to "Current User/Start Menu", navigate to:
%windir%\Profiles\YourUserId\Start Menu and paste a shortcut.
The lower middle pane is called "All Users/Start Menu/Programs". You can paste a shortcut or copy a Folder of shortcuts to this pane by drilling down to
%windir%\Profiles\All Users\Start Menu\Programs. To add a shortcut to one of these folders, simply navigate to the folder or sub-folder and paste the shortcut.
Lastly, as you've already guessed, the upper middle pane is called "Current User/Start Menu/Programs" and is located at
%windir%\Profiles\YourUserId\Start Menu\Programs and is managed the same as "All Users".
As in any other folder or file, you can right click to "cut", "copy" or "rename". Right clicking on a shortcut and choosing properties, allows you to manage the shortcut's Target, icon, "Start in" Hot key and Run by selecting the shortcut tab.