You can add folders to the Manila start menu, but you have to edit the registry as far as I can tell.
Code:
HKLM\SOFTWARE\HTC\Manila\Program Launcher
You'll see a bunch of numbered registry keys, 0 is the first slot on the menu and it counts up from left to right on each row. All you really need to set is the DispName key and the Path key, and you may need to soft reset afterwards to get it to show. Hope this helps.