Your best bet at this point would be to navigate to where IE stores your bookmarks and organize them from inside that folder. IE stores your bookmarks as individual files here: C:\Documents and Settings\your user name\Favorites
Inside this folder are all your favorites and IE's Links folder. Any folders you create inside here will show as folders in your favorites menu in IE so it will be easier to organize them from here then it would be to use software to do it for you. Just navigate to the favorites folder create any topic folders you wish to create and then select and drag your individual link files to the appropriate folders and you are done.
The way I use my Favorites folder is I put all my category folders inside the Links folder because this allows me to have access to my Favorites from the Links toolbars on both the taskbar and on IE's toolbars as well. This allows me easy access to my links both before and after IE is opened.
As you can see you can create folders inside folders so you can get a large number of links inside a small space if you organize your links into categories and sub-categories.
To add the Links tool-bar to the Taskbar simply right click on the taskbar go to the toolbars option and select Links. A shortcut to the Links folder will appear on the the lower right side of your taskbar by the Notification area (the clock). To add the Links option to IE itself right click on an open area of IE's toolbar and select Links on the drop down menu and a shortcut will appear on IE's toolbar as well.
This will still take you awhile to finish but will be worth the effort when you are done.
See you around
There is no justice, there is just us.